To employ a much-used cliché: Politics is a dirty business.
I believe that with the way humans (and, in ST, other species, as well) are made up, it is impossible to cope with some complex and threatening situations, and especially *wars*, without getting your hands dirty. The scale doesn't necessarily have to be as large as when Section 31 tried to kill the Founders, but one way or another, you'll end up doing things you never really wanted to do and that are immoral by common standards (and probably your own).
While I do not believe that Section 31 attempted genocide at direct orders from Starfleet Command or something like that, I can't believe that Section 31's autonomy is complete. (If it is, this would be even more shocking and dangerous than a Section 31 that has at least *some* connection with Federaton authorities, and is thus at least under a *minimum* of control.) Like in any political body and in every government, I believe there is a kind of 'twilight zone' somewhere in the high levels of the Federation government where pragmatism defeats morals, at least in times of extreme danger.
That is not to say I agree with Section 31's actions. I am not judging here, just trying to understand the relations between the 'official' Federation and its more sinister part. It would be too easy to discount S31 as a sect-like, independent organization of political extremists. Starfleet or the Federation government (btw, has anyone ever wondered why we *hardly ever* get to see civilian officials of the Federation???) were, apparently, perfectly willing to benefit of the actions of that group of extremists! Wouldn't the Federation's morals normally suggest that genocide against the Founders had to be prevented at practically any cost? I had basically regarded S31 as just that, a group of independent fanatics, before the point when Sisko told Odo he must do nothing to help the Founders... that was the moment that made me think there *might* be some sort of connection, however inofficial, between S31 and Starfleet...
What point was I trying to make? Give me a moment... I get lost in my own arguments pretty often... ;-)
Err... So: I think SF/the Fed. may have been in the dark about the exact plans of S31, but someone high up very probably had a hunch and did nothing to prevent it. And when the Founders were dying, they (the Federation) were not beyond seeing the advantage it brought them in the war. Would there have been a chance to stop the war if they had given the Founders the cure? Interesting question - I don't really have an answer to it, but I tend to think it wouldn't have stopped the war for long, if at all. And Odo's bringing them the cure wouldn't have stopped the war in any case, 'cause it wouldn't even have been a gesture of good will from the Federation...
So, is the Federation guilty of war crimes, bluntly put? Yes. Hands down. They may not have been the instigators of the whole affair, but they profited from it and did nothing to prevent it. IMO, they were *very* lucky that the whole thing ended the way it did, and not with the Founders dying. If this had actually happened, I don't know what would have happened to the Federation as a whole. This might have destroyed the Federation, in a way.
I think the Dominion War will have a similar impact on the idea the population has of the Federation as Vietnam had on America... I know this is not completely comparable, but still... The war has definitely destroyed a number of illusions for Sisko and Bashir and Nog and Jake and probably everyone else, too. The people who have been really aware of the goings-on will not be able to see the Federation as a near-ideal system anymore.
Okay, so the Federation is guilty. The Dominion did slightly worse, because it not only tolerated genocide like the Feds did, but actively *commited* it, but that doesn't make the guilt go away, does it?
So how do we react? (I know it's only a TV show ;-), but let's assume we are Federation citizens.)
We do *not* excuse what happened - we would have to discard too many of our principles to be able to do that. But we *understand*, kind of. With a sense of sadness but also of acceptance - after the first outrage. Because what else can we do? Start a revolution? What would we change? The Federation *is* one of the closest approximations of the ideal society ever achieved - it's highly unlikely a new system would fare any better.
But how can we disapprove and yet at the same time accept the actions (or sins of omission, in some cases) committed by Federation officials? Isn't that a bit paradoxical? Maybe. But the more I think about things like this, the more I come to believe that RL is all about coping with paradoxes.
Is there any point in this posting? What exactly was I replying to? I don't remember. My mind went off on a tangent, I guess ;-)

Sorry. Hmpf