Boolakanaka

Just as a heads up to others who are curious about who is hearing back from who...
I heard back from Boston U at the beginning of February (got accepted and was offered possibility of free tuition) and I got a phone call from Emory/Candler earlier this week congratulating me on an acceptance (no financial aid mentioned yet). 
Exciting times! Did anyone else get into Emory or Boston? 

From what little I can see of your intents, it seems like you lack focus. How did I arrive at this conclusion?
1. You mentioned that you were accepted into other programs of similar study, which indicates that you do have some background in public policy or some vested idea of what you want to do. In other words, your application's not completely out of left field.
2. Your acceptance to the Graduate School of Education as well as the Graduate School of Design indicate that you're not sure where to go, but you want to go to Harvard. In other words, you sound like you seek the external validation that Harvard Kennedy School can provide.
HKS values two things: impact and focus. You need to tell them, very specifically, what it is that you want to do and how you plan on doing that.

Generally speaking, your distinction between M.Div and MTS/MAR/MA is true. The former is geared those considering the possibilities of ordination or certain doors that may be opened with an M.Div, whereas the latter is considering academia, professional schools, or needing to acquire skills for a niche field, such as becoming a religion reporter. MTS-style degrees tend to have lower acceptance rates and less funding, while M.Div programs generally have higher acceptance rates and more funding, often due to denominational donors. Keep in mind that M.Div programs are three years, whereas MTS programs are two. M.Div acceptance rates at top schools bounce between 40-60% whereas MTS programs are closer to 30-40%±.
My usual advice is that if a student has any inclination toward ordination, religious leadership, or a "ordination if rejected from PhD programs" - go for the M.Div. You'll get most/all of the same courses, you can spend more time with languages, most schools let you cater field supervision to your needs (I TA'ed undergraduate RS courses for a year). In cases where students already have strong grounding in language, solid GRE, and they simply need to check off the "have a Master's" box to even apply - go the MTS route. If you can honestly say, "If I'm resoundingly rejected by all PhD programs then I'd rather go work a cubicle job than work in ministry/non-profit," then definitely hit up the MTS route. Don't spend the extra year and take out the extra loans for work that will crush your soul.
M.Div applicants are a dime a dozen when it comes to applying to PhD programs, it's not going to affect anything. You've had an extra year in school so some parts of your app should reflect how you took advantage of that. If your M.Div wasn't competitive or you didn't feel that it prepared you, there's always an STM degree. The one case where an M.Div might trump MTS/MA is if you were going to propose a field of study that touches on "applied/practical theology," (liturgy, homiletics, some theology fields, some areas of ethics, etc.) often schools and/or advisors will expect you to have an M.Div. 

You'll be a good applicant for any of the programs you've mentioned. M.Div programs are set up to have both second career students with a lot of experience and students right out of undergrad. Your age won't be an issue and your experience will be seen as a strength. Most M.Div programs want to have diversity in backgrounds/life experience in their incoming class and I take it you'll have a lot to offer in that category given your previous work
As for your weaknesses, I think that you're applying to enough schools where even if your GPA hold you back at some schools you most likely won't be rejected from all.