The salt vampire was different. That was only one creature. Sure, it was the last of its kind, but that was irrelevant. The crew were faced with one specific creature who was about to kill a man, thus they are justified in killing *it*. The fact that this would mean the end of the creature's species is incidental.
Picard, OTOH, was presented with a weapon which would not kill one drone which was attacking him (he was not in immediate danger of course), but which was made for the express purpose of murdering billions. That's a whole new ball game.
Genocide is never an answer. There's always an alternative.