I don't see the problem here being anything but yours and it is a non-problem you have identified... You said:

Realistically, her religion won't really affect our relationship at all. She doesn't talk about it or anything, she's the same person as always and everything...

So....it doesn't change the relationship---only your perception of things..

but I'm having a really hard time just being happy with it. I really want to accept it, and maybe it is another problem (I have a hard time accepting people's opinions if they're different to mine, I guess I need to figure that out), but I just can't be completely happy with it. I get really annoyed if I think about her going to church or anything like that, but I want to be happy with her, and be able to accept it, especially as it isn't affecting our relationship at all.

This makes no sense--she has to have other differences already even when she was away from believing in church etc...you two are not matching twins..how is this difference more bothersome to you (for what reasons) then before? It is like being upset that she thinks strawberry ice cream is the bomb or believes a TV show is awesome... You afraid she and you gonna go thru a happy life together but at the end she will go to heaven and leave you in empty nothingness? IF you love her then you let her have her silly belief--respect it like you respect her...because otherwise from your description of things it sounds like you cannot respect or never did respect or care about her except that you felt happy cause she somehow reinforced your insecurity about religion. I despise religion--think it is the biggest waste of time--but if people want to spend their time on it that is not my concern...some folks find value in dogshit--some don't--who cares? There are real things that matter to care about or be concerned for--and if this really has no impact on the relationship as you say--why care? While it may end up being an issue later--wait until that becomes an issue--don't go making it an issue cause of what you are afraid may happen. If this difference does not affect the relationship or plans--then figure out what exactly it is that upsets you--why it upsets you or annoys you - and get over it... Don't go having a moral superiority complex over her for making a choice that wont' affect you and her...or else you will make it affect you and her..and then how are you any different from the right wing christian crowd to goes hating on non believers just cause they don't believe. I think as Agnostics or Atheists we have to be the better ones, the calm and more reasonable and sensible ones here next to those with delusions who act out in anger and their hypocritical "unconditional loving hatred" they express...or else we are no different from them.. :/