Full disclosure, I'm not really in any position that allows me to speak on this matters with lots of experience. That aside, to be honest, there could be as much difference and as little difference between a historian and a scholar of religion. It really all depends on your methodology and what type of work you do. Depending on the person, you really could be producing the same work. A religious studies person could do historical work and a historian can study religion. However, a religion-ist will probably be expected to have a broad knowledge of religion and religious studies and a historian would have a broad knowledge of history, but in terms of YOUR research, I think that's pretty much up to you.
A second consideration that this bleeds into would probably be teaching expertise. Assuming that most of your teaching experience will come from your home department, do you want teaching experience (and thus possibly a job teaching) Introduction to World Religions or World History (or insert whatever disciplinary intro class)?
As for selecting graduate programs, from what I hear, it really depends on who you work with and the type of training you receive in the program. The advice I received is find people whose research you like and apply to work with them. Faculty probably matters more than program (unless you're talking about wildly interdisciplinary programs). As to getting in, well that's a mystery no matter what field. My guess that having little to no prior coursework in history would make it more difficult, but not necessarily impossible? Again, probably depends on the department. Honestly, it might behoove you to just email potential faculty and ask them yourself, which also has the added benefit of them knowing who you are before the application hits their desk.