She's beautiful, a bit strange (in a good way) and funny but she's a Christian and I'm an Atheist and it really annoys me sometimes because of some of the strange things she says. It would be fine if she just worshipped God but she says things like "I know God because he's presented himself to me" or "I've met Jesus".

Run in the other direction. Now. I love hearing an old bluesman growling out a religious song, but I really wouldn't want somebody telling me what she tells you either. It really doesn't sound like she's all that well to me.
I think if you truly love someone nothing would put you off them, but then I’m very old-fashioned. If you already disagree on this before you're even with each other, it doesn't look good.
I could see where you might struggle in the relationship. Especially looking into the future... marriage and everything. She'll probably wanna marry in a church or something, and you'll be like "no way!!". But if you really feel something for this girl, why allow anything to get in between? If you're about to let something as small as kooky comments that she makes, be a barrier to what could be a great relationship, than don't even bother.
The idea of religion is not something I really agree with, and my beliefs are what make me who i am. If who I am fundamentally rejects who you are, how can it work?
Then again, I give my beliefs a lot of importance. You have to see how important they are to you.