Religion is something that is a huge dividing factor between people (as is money in politics.) If you've made it quite clear that it makes you uncomfortable that she does it so often, then she's not respecting your wishes. Since I don't know the other side of the story, I don't know if you're pushing your views on her, but in this context NTA.

Personally I would give it a couple more attempts at reasoning with her, and continue to understand religion is obviously a very large part of her life, but at the end of the day you have a choice. If she's making you uncomfortable than that is toxic behavior; something you'll want to remove yourself from if you don't feel that you can work with her to resolve the issues. Pretty much what I had to say in my scenario was: "I respect and encourage you to continue to practice your religion and I think it's fantastic that you want to pray and do so, but if you continue to do it in my presence to the point of making me uncomfortable, I'm not going to stop you. Just understand that I won't be around if you do continue to do so."

I'm not someone who typically likes to make ultimatums, but being comfortable around each other is a huge thing in a relationship and from what it sounds like, you just aren't comfortable.