Really? I'm honestly surprised. Unless maybe it takes a person of faith to pick up on metaphors that went right over my head. It might be interesting to read it again now, with knowledge of the ending, and see what I pick up that I missed first time round.
I mean, I got that all the bad guys were part of an evil church, that was made obvious from the start, but that's fairly standard fare in fantasy works. No way did that lead me to expect the final reveals of how the world works.