Military targets should be the only valid targets in any conflict. I woudln't be surprised if the people running the propaganda are as much a victim of it as anyone else, I would imagine they would be reflecting the more deeply-rooted attitudes of the populace, rather than inventing their ideas and influencing the people with them from the top-down.

Is there any regime in history where the propaganda used to fuel genocidal campaigns has not already had strong roots in the people targeted by the propaganda (and most likely those producing it as well)?