I love DS9, but Sisko should have been court martialed.

I remain quite annoyed by how the major driver for resolving both the Borg and Dominion conflicts hinged on a very illegal, extremely immoral thing that someone did.

DS9 had the Morphogenic virus that Section 31 unleashed, and Voyager had the neurolytic pathogen.

It being the thing that won the wars in the Federation's favour ends up implying that it would not have succeeded without either of them, and that all their talk of morality was simply pretence.

It defeats the entire point of the Federation existing, as part of them having those moral stances in the first place was that they could succeed without having to stoop to underhanded means like their peers did. It might be a harder road, but ultimately more rewarding.

Going by those two conflicts, if you're in a war with the Federation, and they don't see you as an organic humanoid, they will happily have someone attempt/commit genocide on your populace to win, allow it to happen by inaction, or reward them for it. There's no real difference between the Romulan Star Empire or the Federation, except that the Federation pretends to be moral.

Many DS9 fans seem to think that the show's shades of grey renders the Roddenberry vision on display in TOS and TNG invalid - dismissing it with "it's easy to be a saint in paradise".

It might be easy to be a saint in paradise, but the Federation is proof that it's possible to begin with. It won't be easy, but that hardly means it's impossible.

It's also one of the things about the DS9 mirror universe episode that ticks me off. "Mirror, Mirror" ended on a nice, optimistic, hopeful note, where for the Terran Empire's flaws and atrocities, being ethical was ultimately a more successful strategy, and that with time and much work, they too, could be like the Federation. DS9 throws all that out the window with "Spock's reforms softened the empire, causing its destruction", and the hopeful ending, that anyone, even the worst civilisation seen thus far, could become like the Federation, was ruined.

As it turns out, you can only be the Federation, if you're human, in this universe, with this perfect set of circumstances. Anyone else would be making a fatal mistake.

Its particularly irritating in both those cases, because there's groundwork in both DS9 and Voyager to end the war through other means. DS9's ending of the war could be done through helping/freeing the Jem'hadar, talking with the Vorta, and convincing the Founders solids aren't actually all that bad. Same for the Borg, where Voyager very clearly states many a time that what the Borg seek is perfection, and they believe assimilation to be a manner of achieving it. It would not be a great stretch for Voyager to repeatedly interact with the Borg, and eventually convince them that cooperation is a superior method, gradually pushing toward the end of the war in so doing.

Instead, what we got took the easy route, where the Dominion were forced to the negotiation table in the face of extinction, and Borg civilisation/the Collective was outright destroyed.

Its just a terribly cynical viewing of the Federation, where they can only succeed by being underhanded, or having people "do the dirty work" for them. If that's the case, why does the Federation even exist to begin with? It may as well be an empire like any other.

What war crimes did he commit?