I think it's unfair to call that an anti-religion rant. 2 sentences is hardly a rant. Plus, the comment was about the fact that they had naturally evolved into an atheistic culture, which had now been influenced into belief in a false god, potentially stripping them of what Picard calls an achievement. If anything, this is a pro-atheism comment. Advocating an absence of religion is not the same thing as condemning its presence. Picard has shown on multiple occasions to be tolerant & supportive of all people's beliefs, & in one instance even seems to suggest his own philosophy is not entirely atheist.
The second comment about sending them "back into the dark ages of superstition and ignorance and fear" could be relative to the current context, of them falling into the false god belief, which Picard has been advised will likely cause cultural degeneration. Forcing a false god on these people would be inviting a dark age of superstition, ignorance & fear. Whether he is reflecting on our own historical dark ages, or perhaps one that this culture endured, that statement is not in itself an indictment or condemnation of all religion
To see his remark as such is extremist. All he is saying is he wants to do right by these people, as they have been