The other weakness is that the Bajorans look really silly. The Bajorans think that some guy is the messiah, then some new guy shows up and they decide that he's the messiah instead, then they undergo a radical social overhaul that threatens their future security because the new messiah gives a speech. Vedek Birdseye, a seemingly honourable man before the new guy shows up, becomes a remorseless murderer within the space of a week. Even Kira, one of the strongest, most forceful characters in the franchise, just goes along with all these injustices because some guy said so. This is one of the best anti-religion episodes Star Trek has ever done, but I don't think that was its intention. We needed to see more division among the Bajorans, some sense that this caste system nonsense was heading toward a civil war. As is, they hardly seem like they're worth saving.
You're right about their should been more strife and discension, but Bajorans are spiritual to the point of insanity. I think that is because there is direct evidence of their gods, and the Emissary is probably the closest they'll get to 'knowing' their gods. Personally I think it is quite powerful that Kira's beliefs are such that she abandons her job just so she can be an artist, and that scene which shows how hopeless she is at art shows just how screwy and crazy it is implementing a caste system upon a culture. If anything this episode was not so much anti-religious and more anti-caste system, it even openly attacks the caste system so it is bold this episode.