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."