Perhaps I was overtly harsh.
SISKO: Nobody's saying that there can't be spiritual teaching on this station, Major, but can't it be in addition to what's taught in Mrs O'Brien's classroom?
KIRA: But if she's teaching a fundamentally different philosophy
KEIKO: I'm not teaching any philosophy. What I'm trying to teach is pure science.
KIRA: Some might say pure science, taught without a spiritual context, is a philosophy, Mrs O'Brien.
SISKO: My philosophy is that there is room for all philosophies on this station. Now, how do you suggest we deal with this?
But this is basically Kira espousing the bullshit stance that science is just a sort of religion, and Sisko agreeing with him.This rubbed me the wrong way.
And yeah, the episode is not so much about who's right than how to deal with the situation. But I really would have preferred if the 'creationism' argument had been defeated on its intellectual merits (or lack there of) instead of by the person espousing it turning out to me a murderous crook.
I don't see that as Sisko agreeing with her, I see as Sisko trying not to get into a fight about it and trying to feel her out about whether she (and her people) would really be completely unwilling to accept any sort of compromise. He's looking for a way out that doesn't cause even more friction. And he's also just very careful about what he says early in the episode because he doesn't fully understand the Bajoran pov yet. Kira even throws those words back in his face when things escalate and he starts taking actual action against some of the Bajoran tactics. And Sisko also gets more assertive with Winn later on after finding out the extent of her influence is much more marginal than was first suggested. It's very political of him, but again, that's literally his job.
And it's worth pointing out that while we're never specifically told if Kira fully changed her mind on the issue, her faith was shaken and she did at least back off of it, along with all the other local bajorans. The school reopened with no changes.
For what it's worth I agree I would've liked to see something other than a murder mystery lead to the break-through, but I don't think it's utterly without value to have something like that as a giant warning sign to wake the creationists up about the consequences of their actions - specifically that they were giving into othering and demonizing non-believers, and that never leads to anything good. This is the message the episode was going for in regards to the violence:
WINN: You live without a soul, Commander. You and your Federation exist in a universe of darkness and you would drag us in there with you. But we will not go.
SISKO: You have just made your first mistake, Vedek.
WINN: Have I?
SISKO: The Bajorans who have lived with us on this station, who have worked with us for months, who helped us move this station to protect the wormhole, who joined us to explore the Gamma Quadrant, who have begun to build the future of Bajor with us. These people know that we are neither the enemy nor the devil. We don't always agree. We have some damn good fights, in fact. But we always come away from them with a little better understanding and appreciation of other. You won't succeed here. The school will reopen. And when your rhetoric gets old, the Bajoran parents will bring their children back.
And while I think it could've been done stronger, it is definitely there as is.
I personally don't see how showing Winn being devious and planning to kill Bareil sends the message that creationist people are wrong.
The episode just illustrated the opposing views without saying which was right, and lst the audience make their own choice. DS9 did that very well.
The entire episode is about creationists being easily manipulated by a psychopathic liar. And it goes out of its way to tell as much of the story as possible from Keiko's pov, deliberately marking her as the hero of the story, while Winn is unquestionably the villain and Kira, the only creationist character who acts reasonable enough to not be a villain, is very marginalized and only brought in to display her position a bit and then to back off of it at the end. It's in no way positive toward the Bajoran position.