Souls get imprisoned with necromancy and even if they get free will, many of them have altered personalities. Some don’t even fully remember their past lives.
Regardless, maybe killing off some undead individuals isn’t right but it is moral to keep them from organizing. Any extant undead must be singular exceptions. An organized undead is a threat.
You can’t raise any person unless they’re dead first. There’s not much between you and the scourge even if you offer them “free will.” When you’re raised as an undead, you’re kinda trapped. Even Sylvanas in her early days had you go hunt down rogue undead that denied her.