By a strange coincidence I watched Balance of Terror last night, and Kirk acknowledges during the teaser that they recognized numerous faiths.
Well, you're still talking about one man's personal idea of the future, or rather, "the future according to Gene Roddenberry." Yeah, despite his own feelings about religion, there are more indications than not that it was alive and well in Trek since TOS. He may have recanted that in later interviews, but it really doesn't stick, IMO.