Brannon Braga is no spokesperson for Roddenberry's intent for ST as originally developed. The quote is dripping with the kind of revisionist, agenda-driven hatred of religion not seen or suggested in TOS.
When Roddenberry spoke for himself, he said things like: "I condemn false prophets, I condemn the effort to take away the power of rational decision, to drain people of their free will--and a hell of a lot of money in the bargain. Religions vary in their degree of idiocy, but I reject them all. For most people, religion is nothing more than a substitute for a malfunctioning brain," and "We must question the story logic of having an all-knowing all-powerful God, who creates faulty Humans, and then blames them for his own mistakes."
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 the direction of the closing lines 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"
Braga's agenda had him talking out of his ass, 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.