I don't remember a mention of the church being Catholic. The only possible hint I got was in the name ("The Brethren of Calvary"), but that really means nothing. Or perhaps you could be talking about the "precepts of the covenant," but I think other churches have those too, not just Catholic ones (although certainly not Fundamentalists). Do you remember a place in the episode where they specifically said it was Catholic? I ask because I think the writers wouldn't have missed something like that if they really intended it to be a Catholic church.
Edit: Or, maybe there's an issue because they intended for the type of church to be unknown. That way, they wouldn't be picking on any denomination with the drug song and other issues up-tight people might have with the episode.
When I go insane, I want to think I live in the Malcolm in the Middle world.