You should check out the Star Trek TOS episode "Bread and Circuses", about a world of parallel Earth-like development where Rome never fell, but survived to develop Twentieth Century technology, and still persecuted a peaceful sect of "sun worshippers".
From the Wiki description at http://en.wikipedia.org/wiki/Bread_and_Circuses_(Star_Trek):
"Back on the ship, Kirk commends Scotty. Spock expresses curiosity to Kirk and McCoy as to why the slave "Sun" worshipers seemed to adhere to a philosophy of peace; again incorrectly, Spock says that in most societies sun worship is a primitive religion of superstition, with no philosophy behind it. It is at this point that the landing party learn the true meaning of the repeated references to the "Sun/Son". Uhura, who has been monitoring radio transmissions from the planet, informs them that the worshipers are actually referring to a "Son," rather than "Sun," as in, "the Son of God." Kirk replies in realization: "Caesar ... and Christ; they had them both..."
Of course I'm not disputing that ref in "Bread and Circuses", however, Roddenberry the human being in the real universe is on record as saying he himself, the producer, saw a future universe largely without religions. Certainly the individual authors of each episode would put their own thoughts into them, and as a Zinger/surprise Ending, that use of it would be integral.
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