I just picked up a book at the library dealing with the religons of Star Trek. There was a lot of religous beliefs during all of the series. TOS had tons of religous references in it and dealt directly ("Who Mourns For Adonis" for example).
Apollo seemed like an adolescent version of Trelane ("Squire of Gothos") who needed worship rather badly but didn't answer "why?". Looks as if just like Trelane he used people for his amusement like toys and had these kill off one another just like in the legend of Troy. The opening line of the episode could suggest that:
CAROLYN: Here's the report on Pollux Five, Captain. This entire system has been almost the same. A strange lack of intelligent life on the planets. It bugs the percentages.
In general, TOS attacked the petrified beliefs in false gods, but I don't see that much debate regarding actual religious or spiritual matters and IIRC that's one thing Gene Roddenberry wanted to keep out of Star Trek.
The Bajorans were deeply religous and that was a theme in both TNG as well as the entirety of DS9. DS9 was hugely based around religon. Voyager had some religous type themes from time to time.
Wasn't it made rather clear early on that the Bajorans believed the wormhole aliens to be gods? I remember mostly all the conflicts that arose from the religious organization they had set up but not really that any spiritual issues were really discussed or explored.
Nice Trek BBS name you picked.
I'd assume that some BBS members would have felt that should have been mine...