Seriously though, who cares, the relationship worked before, just carry on?
I think when after 2 years things are not what they seemed when you first started it's time to reasses the situation. If someone dropped a bomb on me like that after such a long period I would.
I would consider there was no trust initially, that she was hiding something just to be with me hoping "x amount" of years would make me love her too much to care and be emotionally deluded.
Secondly, if said girl knew I'd take a dislike to the religious side of her so decided not to mention it till later is a massive indication that she was doing it to get her way and not caring about you.
There's two things I can say for sure about people, or mostly women from personal and other peoples experience is that they either.
1; Hope you change after they are with you, not liking the original person you are. Quote the eternal spoken word, "YOU NEVER CHANGE! IM LEAVING YOU!

"
2: Hide lots of stuff until you are years deep into a loving relationship in hopes that you'll forgive them as so much time has passed.
You're lucky if you get 3: She doesn't do either and is a respectable/logical memeber of the human race.
Edit: To OP: As long as you can carry on your relationship as is and she doesn't bring all that crap in it, carry on and let her do her stuff.
If she starts to push her views and ideals, things won't go well.