> DS9 had an actual instance of torture too, but it was a hero being tortured by... half-hero, half anti-hero

If you’re talking about Garak torturing Odo, that seems different than the 24 case because in that instance Garak was explicitly working for “the bad guys”. And even so he was doing the torturing reluctantly and only doing so because the alternative was the torturing being done by another operative which wouldn’t restrain themselves. In other words, in that instance the show was explicitly treating torture as bad.

> made them literally save the entire alpha and beta quadrants, and possibly the entire galaxy, from slow-burn genocide.

Technically it wasn’t the disease which defeated the Founders, though I supposed one can argue it debilitated them enough. Even so, despite the results I didn’t feel like the show was necessarily approving of Section 31 (the main characters actively tried to defeat them).