DS9 had an actual instance of torture too, but it was a hero being tortured by... half-hero, half anti-hero[0]? Not sure that one led anywhere, beyond being a very disturbing way to do character development.
Section 31 angle is tricky, because the writers unintentionally[1] made them literally save the entire alpha and beta quadrants, and possibly the entire galaxy, from slow-burn genocide. The Dominion was known to systematically subjugate and ultimately eradicate solid life, and other than the Federation Alliance bloc (that prevailed only because of Section 31's bioweapon short-circuiting the war[2]), the only power left in the known galaxy strong enough to resist the Dominion would be... the Borg Collective, which wasn't really that much better[3].
So, as much as I love DS9, I feel the show (and the larger franchise) has so much unintentional depth, that most obvious takes don't work with fans, because they don't survive scrutiny :).
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[0] - The simple tailor was anything but.
[1] - At least as far as I recall, Section 31 were written to be the rotten apples that got revealed and removed by the heroes, in a pretty straightforward way - but IMO, they failed at this, and instead created something more of Deus Ex Realpolitik.
[2] - And a little bit of actual fleet-eating Deus Ex Machina, on the account of having a demi-god in their midst.
[3] - And nobody in or out of universe really wants to talk about what happened to the latter, except the last season of PIC that tacitly acknowledged it in a "blink and you'll miss it" way.