The Borg can be somewhat rationalized, since (at least at the point pre-"I Borg") you can make the argument that Starfleet was in conflict with a single entity in the collective. So an attack against the Borg is not exactly one where there's civilians and innocent children who will be affected. Once it became clear that it was possible for a Borg drone to break away under the right circumstances then it became much, much murkier.
But I think even Picard would call what was done to the Changelings a stain that betrays the values the Federation were founded upon.
I mean the Allies hung Nazis and Japanese war criminals for doing the exact same thing, and hunted Dr. Josef Mengele for decades for experimenting on prisoners in the same way.
