THIS. Everybody knows that Roddenberry was against religion; that's part of his script for the aborted Star Trek movie The God Thing (which later became the basis for Star Trek V: The Final Frontier.) When did he say that he was for it, or that Braga was wrong?
What bothers some people is Braga's sweeping statement about Trek in general, particularly TOS. While Kirk certainly did his share of god-zapping, beginning with Gary Mitchell, there is no evidence from that show itself that GR was as totally hostile to to all manifestations of religious belief in the 1960s as he later became.