While the institution itself might not be harmful, and most of the individuals within that institution may be good and honourable people, but blind faith in the institution rather than the God is dangerous. I can't speak for other parts of the world, but I know that in my own country the blind faith that the majority had in the Catholic church was harmful to our society in many ways. On the issue of child abuse, some people had so much faith that the church was right in all things that they didn't believe their own children when they were told of the abuse. Those that did go to the police were often ignored because even the police didn't want to be seen to be taking on the church. The families that did speak out were sometimes ostracised from their communities by those that refused to believe the claims.
Not all institutions are bad or corrupt, but no institution should be excused from scrutiny, be it a government, a private company or a religious organisation. If the majority of people give an institution their blind faith and do not question it then there will be those that join that institution seeking power over others. Winn was such a person, and she was given control over a whole planet because not enough people were willing to question her motives. If it wasn't for Kira standing up against her, Winn could have led Bajor to disaster.
I think that Kira is a good example of a religious person. She believes in the Prophets, she knows that they're real, she has faith that Sisko is the Emissary because he has proven that he is, but she doesn't believe that Winn is good or infallible just because she was elected Kai. She knew that Winn was a bad person, her title didn't matter. If Bareil had been elected instead then Kira would have followed him, not because he was Kai, but because she knew him to be a good person.
