Depend on what you mean by "the Federation." Do the people of the Federation need to be protected and safe? Yes. To that end it isn't a matter of a ego contest with the Federation's authorities, and their ability to say "only we are allowed to protect you." The primary importance is that the protection is being delivered.
War hammer 40K is classic space opera grimdark, there is only dark and more dark and more dark and endless hopelessness. Grimdark is wallowing in depravity, despair, degradation and cynicism that's the whole appeal. Most of popular culture today leans in the direction of grimdark. Stuff with a moral center is viewed as candy fluff. That's a problem with the culture.
Weyoun: "If you ask me, the key to holding the Federation is Earth ... our first step will be to eradicate its population. It's the only way." And there's your justification. Fans (some) also or instead read it as at the end of the day there is a Federation with a massive civilian population that absolutely has to be protected. And that this is the number one ethical imperative. If your moral position is that it better to die to the last man, woman and child rather than violate some ethereal principle then I submit that you're placing priorities in the incorrect order.
Yes, this. Part of humanity is the fact that we all have skewed perceptions of the same fact. I love that TOS examines that and presents morals.
Since total victory is to all intents impossible, crushing your enemies rather than making actual peace will always lead to circular repeated conflict. If it is right to crush an opressor, to then oppress it in punishment, then you continue that pattern...those former opressors become the oppressed, and will of course then turn around and crush those that crush them (see twentieth century history, and in a less violent way, the current political shifts happening) If the federation ceases to be the federation by rejecting its values, what has been preserved? It is still lost. The federation has to 'win' to preserve itself physically, but it has to win in a way which retains its identity to preserve itself ideologically...which is is ultimately what the federation is, an ideology, not anything approaching a nation state.....which is ultimately what it does, and ultimately what Ds9 is actually about, even In The Pale Moonlight. For certain conflicts, fought on ideological lines, you cannot reject your own ideology in order to 'win'. The entire Dominion war is not about destruction....the Dominion wants to rule, not destroy, but Dominion rule would destroy and go against the ideals of the federation. So they cannot abandon those ideals without in fact losing the 'moral high ground'. It would cease to be something like a 'Just' war, and simply become about who has more power, and using that power as a 'right'. Is my moral position to die to the last man? No. But it would be to know, really know, why I would be fighting. Though let's be honest....both sides in any given conflict will consider themselves to be 'right' and 'just' and it's only when you get down to something like an objective viewpoint that judgement can actually be made....even war has rules, and from a human perspective there are some things that are just so wrong that they needs must be fought. But never lose sight of what you are fighting for, never simply replace one oppression with another, if you actually want anything approaching peace. History is full of groups who, having decided they had 'won' against some terrible evil, then forget the how or the why, and fall into another form of oppression, sowing the seeds of their own future enemy. Every empire in history has done this in some way, from Pre-History to the current failings of the Post Cold War set up, even on a simpler cultural and political basis without delving into warfare. And people who say the same stuff I just did probably turn up, and sometimes while societies aim for being magnanimous is victory, and create a peace for a time, sooner or later...the same mistakes are made, and the whole bloody wheel starts turning again. Which is rather crap for those of us out the edge of the wheel. Those comfy in the centre just get a little dizzy. Then of course you can get jaded and cynical about ideals, and then the only right becomes the right of the strongest and most powerful with some force, military, economic, cultural, it doesn't matter. And guess what. You have an opressor again. Which will create its own Nemesis...and...well...you get the idea. And that is why, within the fiction of Star Trek, the Federation cannot allow something like S31. Because then the Federation is not the Federation, and is no longer particularly culturally distinct from Romulans or Cardassians. The Klingons become the good guys by default. And our 'heroes' know that, even Sisko after his brushes with journeying down that dark path.
Speaking of oppressors and oppressing and the cycle of revenge that seems to fit the history of Mirror Universe Trek to a tee. The humans have fought and oppressed each other, oppress the Vulcans and other species, then their oppressed, and(in STO) the cycle repeats itself. In the books Spock has this grand plan you see, that will ensure the Terran rebellion doesn't become Terran Empire 2.0 and oppress the Cardassians/Bajorans/Klingons for oppressing them.
The TOS episode "The Savage Curtain" had an interesting take on the matter of war and peace. This is what the Lincoln character had to say: One matter further, gentlemen. We fight on their level. With trickery, brutality, finality. We match their evil. I know, James. I was reputed to be a gentle man. But I was commander in chief during the four bloodiest years of my country's history. I gave orders that sent a hundred thousand men to their death at the hands of their brothers. There is no honorable way to kill, no gentle way to destroy. There is nothing good in war except its ending. And you are fighting for the lives of your crew. I have no idea if Lincoln's sentiments reflected what GR might have felt. What Lincoln said sounded reasonable. However idealistic one may want to be, it has to be grounded in reality. Spock speculated that Lincoln was created out of Kirk's thought, so what Lincoln said probably reflected Kirk's attitude. Near the end of the episode, the rock creature asked Kirk: ROCK: You have failed to demonstrate to me any other difference between your philosophies. Your good and your evil use the same methods, achieve the same results. Do you have an explanation? KIRK: You established the methods and the goals. ROCK: For you to use as you chose. KIRK: What did you offer the others if they won? ROCK: What they wanted most. Power. KIRK: You offer me the lives of my crew. How moral would it have been for Kirk to not use whatever force is necessary to save the lives of his crew? How moral would it have been for Starfleet to not use just about any method to defeat the Dominion, which was out to oppress the Federation and destroy the way of life of the people of the alpha quadrant? Oddly enough, the Surak character -- the Vulcan who was an absolute peacenik -- met a brutal death. His peace efforts amounted to nothing. I think the TOS writers had a good understanding of the human condition. They framed these kinds of issues into stories that came across as very compelling.