Considering I found the overtly religious crap (Pah-Wraiths and Prohpets) to be the weakest part of DS9, and the confirmation of religion as real in BSG to be what made that show awful (and lets be honest season 2.5 onward was a train-wreck of Lost level proportions, just complete shit.) - I'm still gonna hold it against Moore for inserting those elements into those two shows.

I like the idea of religion existing as a personal, political and culturally motivating force in BSG, but when it becomes an objective reality it's flat-out offensive to the spirit of science-fiction.

In Star-Trek, I felt the Prophets where actually well handled in the sense that the Federation considered them "Worm Hole Aliens" and not gods, but I also felt like everytime they focused on that plot, rather than just using the religion of the Bajorans culturally, the show got worse. Super Pah-Wraith power-up was the dumbest crap ever and almost ruined Gul Dukat. Sisko's character was weakened by making him actually a literal chosen one of the prophets rather than a Starfleet Officer struggling with an alien cultural role thrust upon him by a religion he doesn't accept as true but has to respect because of his position.

Basically, religion as politics and culture as fine, that's realistic and even a form of anthropological SF, but the gimme in science-fiction is the semi-plausible science based in scientific theory - not magic.

If anything I feel like Q was Gene literally making fun of the Judeo-Christian conception of God. He was an avowed Atheist and Humanist, and had despite what you'd think a very cynical sense of humor from years of being military and a cop. Gene took the childlike, tempestuous, jealous, angry, spoiled, vain, irrational God depicted in the Old Testament and made him Q (a 'god' foiled by reason, science and humanity).