Science fiction has never completely turned its eye from religion.
I ought to say that this post here concerns itself exclusively with televised depictions of sf. Literary sf, the written word, is a separate consideration I leave for you as an intellectual exercise.
Star Trek, for one, never shied away from the theme of encounters with any number of "Supreme Beings" and entities demanding worship as deities. Gary Mitchell, after his transformation by the Negative Energy Barrier; the Talosians; the Squire of Gothos (an immature Q?); the planet of Landru; Apollo; the Gorgan; Garth of Izar, gibbering and shapeshifting on Elba II; the degenerate colonists in "Plato's Stepchildren;" the Cheronians, Lokai and Bele; the Q Continuum; the Douwd; the Dominion; the Prophets; the Pah-Wraiths.
And Trek never shied away from the themes of questing after the truth, nor of blind worship and the bigotry that that blind worship fosters, along with the conflicts that bigotry generates. Red Hour in "The Return of The Archons;" Vaal worship in "The Apple," where Vaal even forbade sex ("Well, there goes Paradise." -- Dr McCoy); "Who Mourns for Adonis," where Apollo finds himself out of his depth dealing with Kirk, whose ego turned out to be vast, vast; and those religious fools which held Captain Archer's NX-01 Enterprise to ransom in that show's lamentable third season.
A number of times, the show took religious zealotry to one of its logical conclusions. Twice, to a ruined world - the denouements of "Let That Be Your Last Battlefield" and "Chosen Realm;" and many other times, to the ruination of the pilgrims as they discovered that their Paradise was not as it seemed - the poisonous planet Eden in "The Eay to Eden," the planet Sha-Ka-Ree in That Execrable Film Before Star Trek VI That Must Never, Ever Be Named.
Star Trek was not shy of exploring the primitive side of its most advanced races - the Vulcans had their monasteries, legends and myths; the Klingons murdered their gods, and the monks on Borath attempted to reignite Kahless worship with a clone of the founder of Klingon culture.
Dare I mention the Babylon 5 episode "And The Rock Cried Out, No Hiding Place," with the priests visiting the station, the monks that came to B5 during its third season, the First Ones, Valen, the episode "Day of The Dead" with its theme of the afterlife, and Thirdspace?
Plus of course, deities of various stripe have turned up in Doctor Who. Bok ("Chap with wings there. Five rounds rapid!"); Sutekh; the Ragnarok; Fenris ... The Beast ...
All these "Supreme Beings" have turned out to be, to some extent or another, alien beings of immense power, physical and psychic. But still, alien. Not yer actual Gods. The Organians evolved into energy beings from a more primitive form made of ordinary matter; Lorien, "The First One," was a mutant (B5's Grandfather); and Vaal turned out to be a machine. Even Apollo turned out to be mortal, after all, fading into the wind when he was defeated by Kirk's bloated, planet-sized ego.
"What does God want with a Starship?"
As for it appearing in Traveller ... yes, I can see the problems. Your characters are toying with immense forces: pocket nuclear fusion in the form of the FGMP-15; disintegrators, psionics, teleportation ... and along comes this Sunday School vicar, all G K Chesterton, preaching some sermon about men in frocks and sandals being bathed in water by some river, or they encounter a bunch of men in coloured pyjamas talking on about "purity" and "sin" and "heaven" and "hell" in a world ruled by physics and economics, where everything is measurable and where, in all their travels, Man has not met one single solitary angel riding on a clour, playing a harp. Not even some creature with goat legs and a forked tongue and horns.
Doesn't fit, does it?
The characters might encounter some Ancient matrix containing an alien living entity, vast and cool and unsympathetic in its intellect and power. It doesn't mean they just have to kneel and pray to it, even if it can deflect their ship's lasers with a flake of its mind.
