I'm not going to dig through the whole thread...but that 'OMGGENOCIDE thing' is just moralistic claptrap. Let's say Starfleet discovered the location of the New Founder planet while at the same time developing an advanced cloak. Am I to believe that Starfleet should surround the planet with a fleet and then demand the Founders surrender?
And are the Feds so naive/lacking in Intelligence as to not know that the Founders have no problem with genocide and are more than willing to do so to win this war that they have very nearly won more than once? And it's not like there are civilan Founders. Deciding to kill the Founders should easily carry more moral weight than bombing a city. Or blowing up a garrison.
The point of war is to win. Especially a war as uncomplicated as the one against The Founders. And all this angst over wiping them out is moral bedwetting. It really only makes sense if there ARE civilan/innocent Founders. And for the sake of this argument we will assume there arn't since we never heard a thing about "Oh, you know...many of my people did not want war with the Alpha Quadrant."