The three latest crop of Sci-Fi channel shows all have very deep threads of religion going through them: Stargate SG1, Stargate Atlantis, and BattlestarGalactica.
The common theme seems to be that what people call "Gods" are really just much more advanced beings that posess powers that mere lowly lifeforms will interpret as God-Like.
Stargate SG-1, now has the Ori which are advanced beings that gain power from whole planets praying to them and worshiping them. They must destroy all unbelievers since they sap energy from themselves, and help the enemy.
Atlantis of course have the atlantians, which have shed bodies and are existing on higher plane like gods, but are disinterested in affairs of mortals anymore. They are hands off Gods observing us ants in the ant-hill, while Ori are slave drivers forcing you to worship them.
Also SG1 previously had Gouuld creatures that used technologies to enslave humans as egyptian Gods of past (e.g. Ra, Osiris, etc).
The most complex is Battlestar Galactica, where humankind exists in a world worshiping multiple Gods, while the Cylons machines worship a single true God. And of course Cylons are trying to cure humans of their mistake by making them worship their true one cylon god.
All of this I am sure this audience already know. But just showing that there is a way to weave religion and religious themes and principles into Sci-Fi shows without causing too much trouble. Naturally devoutly religious people will be greatly offended by the idea that Allah, Yahweh, or Jehovah is really just an alien being in a spaceship??
But thats why its fiction. Faith does not require proof, and actually relies on the lack of proof. If God came down from the sky tomorrow and said "I AM HERE", no one would probably believe it was God. So having Faith that he is there is all we have to work with. No proof is sufficient.
I will stop my ramblings now........