So the Federation council officially refused to end a genocide that their own citizens have committed?
Imo the DS9 writers went too far here/screwed up.
I've argued this before, but killing the high command of an enemy nation, regardless of their numbers, is not genocide, at least not under a criminal definition.
The Founders are a species, so the word "genocide" can serve merely descriptive definition, but their peculiar biology and social system makes them a lot more like high government officials than the German people at large. At worst, it's an assassination, although I prefer to think of it as a counterpower attack (that is, an attack designed to disrupt the ability of government to continue functioning, in many ways similar to rapid dominance tactics); it is certainly not a criminal genocide--it is perhaps criminal that the tactic was used as part of a first strike (and that too is arguable). But even assuming the Federation did use it in a first strike, the Federation would then only be guilty of aggression--but not genocide.
An analogous situation would be a British chemical weapon introduced by a secret agent at the Hugo Boss factory in 1938 that gave everybody in an SS uniform cancer.