But wouldn't the federation being destroyed by the Founders also destroy the federation's values from that point forward? Just because you possess a strong moral standing does not mean you then have to permit a enemy to wipe you out ... you know, in order to make some kind of meaningless point on how moral you are. You and your society are allowed to defend yourselves, that defense can include the employment of violence and death. The fact that the Founders were a bunch of loony screaming paranoids about solids isn't the federation fault.
Nonsense. The canon is very clear in establishing the existence of infant Founders -- Founders who are as ignorant and as innocent as any Human infant. Add to this the fact that we know, canonically, that Founders in the Great Link sometimes disagree with one-another ("Broken Link"), and it becomes clear that not all Founders are "guilty." Really? Do you think that might have something to do with why the Federation was waging a vast interstellar war against the Dominion? 'Cos I'm pretty certain the Federation was employing violence and death to defend itself and called that "the Dominion War." But it is absurd to pretend that self-defense automatically justifies genocide -- or to pretend that genocide was in any way necessary to defend the Federation. The choices are not "genocide or be genocided." Also, bear in mind that there is no evidence the Founders intended to commit genocide against all Humans. Rather, we know that it was Weyoun who intended to exterminate the sentient population of Earth; we have no evidence that this plan spread to or was shared by others in the Dominion hierarchy, and we have no evidence that the plan expanded to include the extermination of all Humans rather than just the population of Earth.
But if the extermination of humans was not the will of the Founders, why would Weyoun - a loyal Vorta - believe in it? The Vorta would no more go against the Founders than the Jem'Hadar would. Besides, the Founders ordered all Cardassians to be exterminated, so it stands to reason they'd do the same to humans as well.
It is entirely possible that Weyoun feels free to do something if he does not think the Founders would object to it, even if it is not something they themselves have desired. Again, we do not know whether or not Weyoun's idea ever spread through the rest of the Dominion hierarchy, or if it just remained an idea of his that he never expressed to others. The Founders ordered all Cardassians exterminated because of both the planet-wide rebellion and the Cardassian Guard's defection during the final battle. We do not know that they would order the same thing for Humans.
Scuse me if I get the clones mixed up here, but Weyoun VI was willing to kill Odo to terminate the 'defective' Weyoun V. The Founders surely would have objected, and he knew it.
Yes they would, because humanity would have done the same thing the Cardassians did if they'd been in that place. If the Dominion had successfully conquered Earth, humans would eventually rise up again. And that would invite the same kind of brutal retribution the Cardassians endured. It is clear that the Dominion does not frown on genocide - they did it with the Cardassians, they did it (albeit indirectly) with the Quickening aliens, and they'd have done it to humans as well. It's just what they do.