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The classic 1960's Star Trek also included male-female gender roles that look fairly quaint today. More recent Star Treks have figured out that Christianity as it exists today will just not be a part of the everyday world in the 25th Century.

Contact with intelligent beings from other planets will surely shape the religious beliefs of Earth people. No branch of Christianity today appears as it did four or five hundred years ago (if such a denomination even existed), why should we expect them to be recognizable in a few centuries from now?

For what it's worth, there was mention of God in the original series. I refer to the episode where Kirk was on this planet ruled by Apollo, the last of the mythological "gods."

Seems these space aliens had visited earth and been proclaimed deities by the Greeks/Romans. The ETs evidently said, "Hey? Who are we to argue? It's their planet." And they ruled for awhile from atop Mt. Olympus.

Later, they quit Olympus and left Earth for new digs. The reason? As Apollo mournfully explained, "The people ceased to believe." Read: Christianity freed the Mediterranean Basin from superstition.

At any rate, Apollo, the last of the laid off gods, is attracted to one of Kirk's officers in the landing party. Naturally, she is nothing short of stunning.

Apollo wants her to be his bride and goddess. She's flattered by the attention and is starting to succumb to his Greco-Roman charm.

Kirk slaps some sense into her (figuratively or literally, I can't recall), reminds her of her oath to Star Fleet, her duty to the ship, the price of tea in China, etc. Seems Apollo wants to beam all the crew of the Enterprise down to his planet so they can tend sheep and worship him.

Kirk persuades Landing Party Babe to help the regular cast overthrow Apollo.

Spock soon finds "A's" power source in some poor man's Parthenon -- a backdrop for Apollo's smoke-and-mirrors special effects. The Enterprise Brain Trust figure out that if Kirk, Scotty, Bones and Spock laugh at Apollo's pretensions to deity, it will provoke him into a fury and lead to a galactic coronary.

That is, if Kirk isn't first zapped to burnt bacon like a bug in a patio light.

Hence comes the showdown, and this exchange, which I paraphrase:

Apollo -- "You will kneel down and WORSHIP ME!!!"
Kirk -- "Sorry, but we find one God to be sufficient."

To my knowledge, this was the only specific reference to monotheistic religion during Star Trek's run, though there may have been others.