I think the technical reason for it being introduced was because of Castlevania for the X68000. It kind of clarified that CV1's stage 2 was supposed to be a chapel (given how there were only stained glass windows in the boss room). SotN reintroduced some elements from that title including a chapel-themed level, and it's sort of become a traditional stage ever since.
But storyline wise, yeah, I guess it's more or less a way to stick it to God. Still, SotN's chapel was pretty...holy, at least once you take out the monsters. In the other games, not so much.