psstein

There is no such thing as a safety school for PhD work. Don't go to a program just because it's the only one that will accept you.

You mean school rankings that measure UG education? Irrelevant.
Graduate education does not work like undergraduate education. First, the application process is not centralized. You are not admitted to a school, you are admitted to a specific program. Your admission depends on many, many variables aside from your credentials. For instance, it depends on who else is applying. If you are an Americanist and fifty other people are applying to that same spot, your chances are less favorable than the five Latin Americanists (gross oversimplification). 
Second, rankings in grad school take into account faculty research productivity, which is a good thing but not entirely relevant to you. You want your specific advisor and the faculty you'll be working with to be active in terms of research, but the whole program ranking averages research in general.
Third, "fit" has become one of those words that we think we know what we mean, but we actually don't. Or at least I don't know how would anyone define it beyond being interested in more or less the same themes, say gender and violence in medieval Europe or East Asian environmental history. I was trained by three scholars who did not specialize in my geography (within the field), but had similar questions as I did. 
Finally, as @dr. telkanurumentioned, there is not such thing as a safety school in PhD work. 
 

I wonder if how much it matters that Kruse works in a huge field at a huge department. In my field, where there are great programs that have only two professors who can train students, reaching out before applying seems more valuable.
 
I certainly would not advise anyone to try to schedule a Zoom call in their first email.

Have questions. 
You need to figure out numerous things, from how engaged a possible advisor tends to be to where their students are now. Often, figuring out ways of getting answers without directly asking will result in better answers. 
Basically, figure out what you think you need to succeed in a program, and what you want from it. Then figure out how to get that information from a source which is likely to paint a rosier picture than reality (intentionally or not) if confronted directly.

If you are at all interested in academia after you finish your PhD, don't bother with online programs. They're not worth it.

You'll have to go to Evangelical Seminaries & SBC seminaries.
University based religion programs mostly fund their Ph.D candidates, so they are looking for strong full time students.
Most Evangelical Seminaries look for students eagerly, so they try to meet the needs of their students. 
What are your goals after Ph.D? If Academic is your path, I wouldn't recommend going into a program that is fully online. The online programs are just not that competitive. 
If pastoral work is your thing, and you want to stay at a church and also fulfill education, look for evangelical seminaries. 

Your chances aren't 0 but you're seriously hurting your chances by not having an M* degree. If you're wanting to be competitive take your pick - HDS, YDS, Chicago, and maybe 1-2 others for the purposes of comparing financial aid offers.
It use to be that the top schools set aside a single slot for an exceptional undergrad student but those students are rarer and rarer. Too, you often saw them in history or some field that I just broadly refer to as 'cultural criticism.' By and large most undergrad students just don't have the languages fully under their belt for a PhD for NT or HB.
Your languages are good. Russian is a bit of an outlier but perhaps it's pertinent to your research interests. If you're at a T5 school I'd look for a language a bit closer to your field. You'll need a basic familiarity with translating written French but given your language exposure, self study.
Also if T5, you have access to faculty that are perhaps sitting on a PhD AdCom in religion and/or have worked with students that have gotten into such programs. They'll be far better sources of wisdom.

Yes, I think the issue with supervision might be significant. I've seen some PhD dissertations from UCL that do align with my interests, which indicates that I could find a home there, but reading the the course syllabi does not make me particularly excited to study there. 
Long-term goal? Possibly starting a history PhD in ~5 years, though I don't think that the history of medicine will necessarily be at the crux of my career (I work in healthcare). Outcomes matter less since I'm not planning on continuing in academia immediately, but it would be nice to develop a project that I could eventually publish. I feel as if I might have more support at Manchester vs UCL. Overall, it seems that UCL is more recognizable internationally but that Manchester is very well respected in the history of medicine community. 
I think the questions I need to is whether I spend the year living in London, doing a course I'm ambivalent about, but with access to world-class archives, seminar series etc, and everything that is London (probably idealized, but I've loved all of my experiences there), or living in Manchester doing a course I find very interesting, in a city that is also nice, but does not have the same level of educational or experiential amenities that are offered in London. However, I was clearly prepared to not live in London and go to Oxford if I had that option, so maybe geography doesn't matter that much. I don't know!

What is your long-term goal? UCL has practically zero interest in history of medicine (they've managed to completely exorcise the ghost of the Wellcome Unit) and I think getting competent supervision would be a significant challenge. With that said, I would try to determine the outcomes for each program. If one program is pumping graduates to Oxbridge or other high quality programs, and the other isn't, then the answer is clear.

I can't say that my MA helped me get a job, but it did make me a stronger person and a better scholar--and helped me realize how much I can accomplish on very tight timelines.  This last portion, while it probably didn't help me get a corporate job that I kept for four years (finally leaving to return to school for an additional undergraduate degree in another social science field), probably gave me the skills I needed to do that job, which involved a lot of client-deliverable writing, deadline-setting and keeping, and organization.  If you're in a MA program that requires a thesis project, you will pick up these kinds of skills that will look good on a resume and are something you can speak to in cover letters in the future.

I'm happy to go into greater detail in PMs, but you should definitely read some of the major journals like Bulletin for the History of Medicine and the historical sections in Public Health Reports.

It's summer, so many faculty are checking email infrequently at best. Don't be too discouraged if you don't get a reply, just try again in the Fall.

Additionally, right now many folks are doing digital humanities which, for some, includes big data or quantitative methods. Maybe you just need to polish your search terms. 

This is a good place to start from. You've honestly outlined a lifetime of work, which is good (in the sense of having quite a lot to look at), but bad in the sense of needing to narrow down further. You might also want to look at James Colgrove's State of Immunity: The Politics of Vaccination in Twentieth-Century America, as well as Karen Walloch's The Antivaccine Heresy: Jacobson v. Massachusetts and the Troubled History of Compulsory Vaccination in the United States.

Thank you for the advice! I want to focus on organized resistance to public health movements. My interest lies in uncovering how public education has become a catalyst for antiscience thought. Fighting against compulsory vaccination has always started with schools. If you've read Kim Tolley's School Vaccination Wars, I was greatly influenced by it. Situating that debate within the Progressive Era and its many restrictive social movements is where my main points lie, but the timeline of education/health is vast (as you mentioned) and I don't want to marry myself to one time period. However, the intersection between religion and social movements are exactly what interests me, as they are so clearly represented in the response of parents to compulsory vaccination in schools throughout history. I'm hoping to find a department that will allow me to work interdisciplinarily.

Are you interested in a specific demographic group in the United States? It sounds to me that you may be crossing into Spanish-speaking and Black communities with your interest in medicine, law, and healthcare. As @pssteinindicated, you will want to do some secondary source readings to see what's already out there in your areas of interest.  For example, I particularly enjoyed works by Laura Briggs, who focuses on transnational connections between the United States and Latin America with regards to reproductive health and rights, children, and power.

Data point: I have a BA/MA from Harvard, and a PhD from Brown. I also have a prestigious 2y fellowship from my sub-discipline's national association and four journal articles either published or forthcoming, many conference presentations, a papal license in a Hilfswissenschaft, and have been in charge of one of the larger DH projects in my field. 
I have applied to 30 positions this fall, from TT jobs to post docs to CC jobs, DH jobs, NTT teaching positions, and library positions. I have made it to one shortlist (still interviewing) for a postdoc which pays less than I make now as a grad student. As far as I know, my recommenders were never even contacted for any of the others.
 

I can answer a few of your questions here.
1) No, there aren't. The market is so horrific that Harvard/Yale graduates are fortunate to get R2/R3/PUI jobs. In the past, regional universities had a very strong reputation for placing PhD students into places like Kent State, SUNY Albany, or a myriad of other state/regional institutions. That market, post-2008, and especially post-2014, is drying up. I don't think the figure of "50% of all colleges will close in 10 years" is correct, but there's undoubtedly a significant contraction occurring. Your intuition and information is 100% correct. There are a few places with one or two faculty members who pump out TT faculty left and right, but otherwise place rather poorly.
2) I'm not quite sure what you're asking in your second question. Yes, you do need to teach, especially as an independent instructor (TA-ing doesn't count for much). With that said, someone with a CV full of grants/fellowships is more likely to have an impressive publishing record, or a very interesting project. Many senior graduate students fall into what I call the "teaching experience trap," which is "I need to teach X more courses before I can be a competitive candidate," often neglecting the dissertation in the process. If you have 2 classes as instructor of record, 4 isn't going to help you. To put it a different way: you can out-publish a mediocre teaching record. You cannot out-teach a poor publishing record.
3) I am and I'm not. One of the things I do in my day job is forecasting intermediate/long-term supply and demand. I think the issues are twofold: first, the oversupply of PhDs shows no sign of abating. While I firmly believe that 90% of PhD candidates have no chance at an academic job, I also don't see the field adjusting for that fact. Second, COVID has been disastrous for universities. Multiple SLACs have had to make difficult cuts in the name of paying existing faculty/staff and keeping the lights on. Smaller institutions (under 3000) are in a very tough position right now. That's also where most of the jobs have historically been located.

I know faculty like that as well. I had one professor who didn't take students for 5+ years, because of how brutal the job market in his sub-specialty looked. It's flawed reasoning, but I also think it's very realistic. The market isn't likely to get much better. University education is fundamentally changing in the US, and not for the better.

I can answer a few of your questions here.
1) No, there aren't. The market is so horrific that Harvard/Yale graduates are fortunate to get R2/R3/PUI jobs. In the past, regional universities had a very strong reputation for placing PhD students into places like Kent State, SUNY Albany, or a myriad of other state/regional institutions. That market, post-2008, and especially post-2014, is drying up. I don't think the figure of "50% of all colleges will close in 10 years" is correct, but there's undoubtedly a significant contraction occurring. Your intuition and information is 100% correct. There are a few places with one or two faculty members who pump out TT faculty left and right, but otherwise place rather poorly.
2) I'm not quite sure what you're asking in your second question. Yes, you do need to teach, especially as an independent instructor (TA-ing doesn't count for much). With that said, someone with a CV full of grants/fellowships is more likely to have an impressive publishing record, or a very interesting project. Many senior graduate students fall into what I call the "teaching experience trap," which is "I need to teach X more courses before I can be a competitive candidate," often neglecting the dissertation in the process. If you have 2 classes as instructor of record, 4 isn't going to help you. To put it a different way: you can out-publish a mediocre teaching record. You cannot out-teach a poor publishing record.
3) I am and I'm not. One of the things I do in my day job is forecasting intermediate/long-term supply and demand. I think the issues are twofold: first, the oversupply of PhDs shows no sign of abating. While I firmly believe that 90% of PhD candidates have no chance at an academic job, I also don't see the field adjusting for that fact. Second, COVID has been disastrous for universities. Multiple SLACs have had to make difficult cuts in the name of paying existing faculty/staff and keeping the lights on. Smaller institutions (under 3000) are in a very tough position right now. That's also where most of the jobs have historically been located.

Thanks @psstein, incredibly helpful (and sobering) thoughts as always. Sorry for the confusing second question, you tackled the spirit of it, which is basically, is there any upside to a program with higher teaching expectations (my read of your answer is, no, and especially not when you factor in all the other stuff that tends to be correlated with).
Your point on the challenges facing the demand side makes a ton of sense. Stepping back, the % of people with any kind of tertiary education in the US is so much higher than in most of the rest of the OECD . . . with seemingly little to show for it in social mobility, a more enlightened civic culture, or human fluorishing. So no argument from me that humanities enrollments (and therefore faculty FTEs) seem doomed to a long decline. Reading comments from more experienced folks on this forum always makes me think I should look into shoehorning my interests into a policy or urban studies SOP ? though a lot of us probably do need to be scared straight!

@TMP's response is exceptional, so I'll use it as a springboard.
1) Very broadly speaking, the majority of programs enrolling 15+ students a year are state universities which depend heavily upon graduate student labor (between TA, RA, admin, and lecturer appointments). Wisconsin, Michigan, and several others fall within that category. Bluntly, I don't think it's a good model, especially in this atmosphere of belt tightening and financial insecurity after one of the most impactful pandemics in a century. The best examples I can think of with your "smaller" model are dedicated history of science programs like Hopkins (which never has more than 10 students), Harvard, or Penn's HSS.
2) The historical reasons fall much along the same lines as #1. Some universities have historically used their graduate cohorts as a replacement/substitute for other labor. Think also in terms of stated university missions. Hopkins was, like Chicago, founded as an American equivalent to the German research university model. The university almost explicitly exists to facilitate research. Compare that to somewhere like Wisconsin, where one of the major principles is helping bring knowledge to the people of the state of Wisconsin.
3) This area I'm more hesitant to speak on, as I don't have a ton of knowledge. I'll say that the biggest obstacle for some of the research-focused programs is getting out of that area when it comes to PhD applicants. I had a faculty member tell me during a conversation "we prepare students for an academic career," which, while understandable, showed a disconnect with the field as it currently exists. The vast majority of your PhD students will not have academic careers! Some programs have very entrenched cultures; Wisconsin's was also rather teaching-centered, and it was very common for students to take quite a long time to complete (7+ years for US history PhDs, longer for European).

I'm hesitant to put a number on it, but for the sake of argument let's say a program which takes more than ~10 per year is either painfully ignorant of the past 20 years of academic hiring trends or deeply reliant on graduate student labor. Or both. I haven't looked in a while, so IDK how many that is.

Also worth noting that the vast majority of historians of science teach (e.g.) early modern France with history of science on the side. There aren't too many dedicated historians of science outside departments like Princeton/Harvard/Yale/Hopkins.
To OP: you're asking basically two questions, one is about the history of public health/medicine and the other is about the development of a social/cultural movement. Asking questions about the development of a vaccine (how did they acquire the materials, how was it tested, why did it fail, how did public health officials react, and so on) are questions for historians of medicine.
I would also submit to you that there's a vast, vast literary corpus on public health education as parts of public health campaigns. If this is the area you're most interested in, I'd recommend reading the major journals (e.g. Bulletin for the History of Medicine) and seeing the recent developments in that area.

One, you're thinking about PhD applications as if they were undergraduate applications. They're not. Teaching at an inner-city school, being a tour guide, your volunteer or extracurricular activities, are not things doctoral admissions committee will really even look at. Your GPA is perfectly fine to get someone to actually spend some time with the rest of your materials. Whether or not you get into a program pretty much hinges entirely on your articulation of the questions you want to pursue in graduate school and your own perception of yourself as a scholar. 
Reading the above, it sounds to me like you'd greatly benefit from taking some time off from school. Secondary education and history of science are wildly divergent topics. Ask your potential recommenders to write letters and stick them in a drawer for later, finish your undergraduate, go work for a year or three, and then ask yourself if you really want to pursue a PhD, and in what area.