I loved 'For the Uniform' so much on the first, like, 20 watches. I think at first my main reaction was "finally, a captain who will go a bit crazy to get the job done. Boy oh boy was the Picard method boring". My reaction now is more, "hmm, I dunno, this seems like a guy got super mad and then massively abused his position of power and did literal chemical warfare just to piss a guy off". The episode doesn't quite commit to calling Sisko out on his bullshit, which is maybe the point (oh we do love some ambiguity don't we; more giant space babies à la 2OO1 I say), but it allows people this wide range of possibly-yikesy interpretations.
Which brings me to DS9 writer Peter Allan Fields. When his name pops up I know I'm in for a good time, and he seemed to love writing these complex morality plays that often didn't really have an answer. Episodes he worked on include "Half a Life", "Dax", "Progress", "Duet", "Necessary Evil", "Blood Oath", and, of course, "In the Pale Moonlight". All of these episodes show characters dealing with the question of whether you can/should break moral/cultural rules for the "greater good", whatever that means. The lack of an answer to many of these is great – you can burn hours thinking about the "right" thing to do, and whether our characters were justified, and come away with a fresh appreciation for the wild complexity inherent to being human or whatever.
That said, I think a bunch of these stories are let down by the bias of the Trek universe. You could say that "For the Uniform" asks us if Sisko is right to do chemical warfare in the DMZ to try to capture a Maquis leader. And... of course he's not. Lol no. But that's not the question: we're being asked if Sisko was right to do chemical warfare given that it nabbed him a Maquis leader. A lot of these stories do this – we see our heroes do terrible things but we then invariably see the positive results. Normally this is because failing would mean our heroes' being either killed or fired, and we can't have that, so the consequence is that we're left to ponder whether doing these terrible things is all ok actually, since it's always been worth the cost so far. I don't really like the consequent implication that the "right" people are allowed to rise above such plebeian concerns as 'morality' when figuring out which rules they plan to break to achieve an assured victory.
'In the Pale Moonlight' is maybe the most 'on the nose' of these stories. I'm all for the closing sequence where Sisko rationalises his bullshit before deleting his log (I adore that cut to black ending the scene instead of the usual fade out – surely just a coincidence that cutting without a fade became the standard only a few years later), but it reads differently when it's the rationalisation of someone who manages to see out the entire show without making a "bad" call. A review of the episode said what made it appealing was that the viewer keeps waiting for the "Federation ideals" to rescue Sisko from the crisis, but they never come, and people die, and then the credits roll. I agree with this, but then you keep watching, and following episodes reveal that Sisko's gamble pays off, and the Romulans join the war, and they win, and there's never any fallout, and it's as if those "ideals" had kicked in after all. DS9 ultimately does the same thing as TNG: the universe regularly bends to the will and wishes of the captain. In that framing, 'In the Pale Moonlight' isn't special – it's just the point where the righteous captain's jurisdiction first went galaxy-wide. Sisko shouldn't have got away with that.