Since your case is peculiar (being that you are already at Duke and looking to do an MA there) you should probably shoot an email to the director of their grad studies and ask him specifically about your case. Many PhD programs don't have a standalone MA but grant the degree en route to their PhD students, and Duke may be of this ilk. If that is the case, they may still be able to work something out for you though, I can't be sure but it doesn't hurt to ask and try.
Regarding other programs and theology/philosophy of religion in general, it is important to consider whether your desired approach is analytic or continental. Again I'm not sure, but I imagine schools with standalone MA programs will not discriminate against you because they mostly claim to support students who apply with the purpose of going on to seek a PhD in philosophy or "in other fields", although you would want to specifically show how your educational goals are philosophical in particular in your application, as these programs can be quite competitive.
The Catholic universities are good in philosophy of religion and theology and generally approach philosophy from a Continental standpoint (Heidegger, Phenomenology, Existentialism, etc.). Franciscan University has a stand-alone MA that is theologically geared and Continental, and you can find a list of Continental-friendly programs at spep.org. As to whether GRE scores matter, this is a point of dispute even on blogs where philosophers comment (leiter's blog), so it depends on the faculty and can vary. The most important thing will be letters and your writing sample, so if you have a good writing sample that shows you can deal well with complex ideas and present them clearly, you should be fine. If you prefer more analytic approaches to philosophy of religion or metaphysics (like those of the Christian philosophers at Notre Dame such as Alvin Plantinga or Peter van Inwagen), then I'm not quite so sure which stand-alone MA programs are good. I'm also somewhat interested in philosophy of religion, and as far as I can tell so far I have found that the Catholic Universities are great for taking philosophy of religion seriously, and that they do this along with taking Continental approaches seriously. If you're not sure which kind of approach you may like, consider looking through an article or two by Plantinga as representative of Analytic philosophy, and something by Paul Tillich for a Continental approach to philosophy of religion.
Hope this helps and best of luck.