I don't understand what the anger in the last round of exchanges is about. Yes, in fictional universe terms, Section 31 is justified. That's not the issue. The issue is why we should give a shit.
You could divide this into the question of whether the story, both plot and characters, are emotionally coherent and thematically consistent, what you might, objectively speaking, well written. Which is to say, something we can invest in. I don't think so, which is not surprising considering DS9 was Berman's first real series. But lots of people here like the series. In fact, much of the arguments seem to be motivated by an effort to defend the show's writing.
But the other half of whether we should invest in the show has to do with how it relates to our lives, experience and worldview. In this realworld context, all the the eeeeeevil Founders and their supernatural powers are bullshit. It doesn't matter whether you can tease out a few lines suggesting that there may be innocent Founders. Once the Founders were conceived as the kind of menace they posed, an hysterics' nightmare, the argument for genocide is made. And it implicitly mooted the possibility for reality, especially since the overall storyline borrowed so much from realworld history. Whether you consider this grounds for rejecting the story depends on your esthetics, whether you deny that morality is irrelevant to art and/or entertainment.