Usually those movements intend to remove "evil" people.
"We weren't evil, how can attacking evil people be evil?"
You can see people say things like this even today. The evil in these cases was done by the people convincing the masses that the other group really is evil and needs to be attacked, not by the masses. The masses will attack and punish whatever they think is evil, everyone knows that, doesn't mean that they are evil, rather it is always evil to label large groups of people as evil since it encourages the masses to attack those.