I'll just mention something I once posted about Biblical references in TOS and the advocates of the "Roddenberry=atheist" missed the following along the way:
In the book Lou Scheimer: Creating the Filmation Generation (pg. 99), Scheimer recalled something telling, which the hardline, "Roddenberry=atheist" group did not know, or choose to ignore:
Gene got to be close to us all at Filmation. I remember when he and Majel barret had their little baby, Eugene Wesley Roddenberry jr., they invited us to the christening. He had a rabbi there, and a Catholic priest, and a Protestant reverend. He said, "There is no way that this kid is not going to go to heaven."
That was not a joke or stunt. Even if one argues that GR's invitation to the reverend, rabbi and priest implied he was not sure--he still moved in a conscious direction of faith the atheist would not even entertain.
With EWR, jr. born in 1974--long after TOS and just at the end of TAS' production, Roddenberry's statement--at one of the most important moments of his life--paints a clear picture that he was not the atheism cheerleader of latter day revisionist accounts, and certainly not during TOS' production. This explains McCoy saying "Lord, forgive me!" a moment before he Phasered "Nancy" in "The Man Trap", or the closing lines about Christ in "Bread and Circuses," which never read like the mere offering of opinion on a parallel event (in the way one would say, "oh, they just invented the car--cool!"), but some kind of deeper recognition/connection.
GR clearly did not like the false god types (Apollo, Gary Mitchell, et al), but TOS was not anti-God, or the series characters having no belief in God (ex. Kirk's line "We find the One quite adequate"), nor was the acknowlegement of the Bible / religon forced on TOS by sponsors or NBC.
Post-TOS advocates for atheism in TOS (such as Braga) have a clear agenda, which has them talking out of their asses. Theirs is an agenda which ignored experiences and 1st hand accounts where GR expressed faith--in order to paint him as the TV producer version of Dawkins