I think the reason is more like that:
Religion in Civ4 is essentially a tool to create power blocs - relationships between civs with a shared religion are better and vice versa. This is further enforced by the fact that there are "only" six religions, but you usually have more Civs, making it almost certain that some Civs ally.
The happiness and extra gold aspect are relatively minor mechanical ramifications - that could be a generic wonder/building/whatever (sure, flavour-wise, it's *not* the same, but just going by flavour... is the way to bloat).
So, if they indeed amped up diplomacy to ensure a natural development of power blocs, the niche religion was filling would vanish. So, I assume they did the bright thing and resisted to put in religion just for its own sake.
It's more likely that it will receive more attention later (much like espionage in BtS) to become a full-fledged subsystem, once the core game works fine. And while I already miss religions from a flavour point-of-view and the distinctiveness it brought, I prefer them to keep the core gameplay tight and good before tackling new subsystems (which is traditionally something for the expansions).