Star Trek and the lack of God

I've loved the original Star Trek series since I was very young. Now, being older and Catholic, I find myself looking into the nature of Captain Kirk's perception of the universe more critically.

The nature of God (specifically as part a monotheistic faith) is hinted at very briefly in only a handful of episodes. In one episode, "Who Mourns for Adonis?", Kirk and company are forced to give worship to an ancient Greek god, Apollo. In the end, Kirk vanquishes the god, telling him, "We've outgrown you." Apollo, virtually powerless as a result of the Enterprise's destruction of his power source, literally fades away, saddened that mankind no longer needs gods.

Gene Roddenberry was big on the concept of humanism...the philosophy that man can discern their own morality, self-worth and respect for others without supernatural or transcendental means. For Star Trek, it's a powerful philosophy that works only because of a strong captain, crew, and immensely powerful starship that could devastate a planet's surface all by itself if the captain willed it.

But we're not Captain Kirk. We don't have incredibly intelligent first officers to explain the otherwise unexplainable, or powerful technologies to pierce through the guises of god-like creatures to explain their true nature and intentions.

And while Kirk's universe appeared to write off the preternatural, explain it away to evil aliens or other beings that once posed as mythical beings of Earth's past, followers of Islam, Judaism and Christianity in the real world know, through faith, that evil does exist.

Star Trek is not alone in the use of humanism, of course. Pick your finest science fiction story and you will likely find how God is, at the least, minimized there as the human (or humanoid) characters take point to solve a problem.

I realize that asking God to step in to solve problems in most stories would result in terrible fiction. (It's an ancient plot device for which this blog's name is based.) It's just something I'm throwing out there to think more about.

What stories could be improved with more than a terse mention of faith and not a synthesis of humanism? Can you think of any examples where faith is mentioned positively and affects the storyline without turning the tale into a deus ex machina situation?

I can think of one show at the moment.