To me what the Bajorans did seemed more akin to underground resistance movements in Nazi-occupied Europe. Of course innocent people died because of their actions, but if the government you're fighting sets up concentration camps, you might get less selective about your targets. I don't know much about war, but I know that guerrilla tactics are always messy.
Perhaps in a remake we would see more of a dark side to the Bajoran Resistance? It was hinted at occasionally, like with Kyra's story were she accidentally shot that mother animal nursing its young. Had the show been made today Kyra might talk about the time she actually shot a Bajoran mother nursing her child.
I thought DS9 handled the religious issues pretty fairly.
Yes, Winn is hypocritical and evil, but Kira is a lead character who is sincerely devout and a good person. I'd argue that Kira is the best depiction of a religious character ever done. That her religion is fictional doesn't take away from how well her character is developed and how well done the religious story arcs are. Sisko makes a point to Jake about respecting the beliefs of others even if you don't agree with them. The finale was the best episode of season 1 in my opinion.
I don't know if you meant me. Yes DS9 treats religion very fairly, except in that one episode imho. I have no problem with Vedek Winn being evil and hypocritical, people like that exist in any religious movement.
It just annoyed me that it came down to the old "Science vs. Religion" and everybody picked a side and stuck to it. Even Kyra admitted that she thought Winn had a point. I personally always cringe at that particular debate because people often paint it as a black/white issue: "if your religious, you can't accept scientific theory", "if you are a scientist you have to dismiss religion as a fairy tale". In those debates I always end up square in the middle with both sides yelling at me or telling me I can't accept current scientific theory while also having faith in a higher being.
That's why the episode made me cringe, not because of the way Winn was portrayed. As I said, I know people like her in my own congregation, just as slimy and just as two-faced as her abd just as hypocritical. However she is also pretty much a medieval/renaissance bishop in space and quite accurate in that portrayal. That makes her interesting, those were the people that caused Luther to break with Rome.