In the episode, "Who Mourns For Adonis""Who Mourns For Adonis" Kirk gives the line, "Mankind has no need for gods. We find the one quite adequate."
I read somewhere that this was inserted at the insistence of the producers who wanted to maintain an Abrahamic religion at a minimum. One would also point to the many scenes in the chapel throughout TOS for essentially the same reason. enter link description here
And then: (enter link description heresource)
"In the 1960s it may not have been opportune to create a decidedly atheist TV show, so Roddenberry may have been forced to drop (anti-)religious references to keep it at least secular."