Not all kishin eggs are people who become them by choice. I've seen it before as did plenty others. Shibusen rewards their destruction because it will make its allies become stronger and they react pretty nasty if you ask them the right kind of wrong questions.

I'm not saying the witches are the good guys 'cause they aren't, but I'd be wary of taking Shibusen's words and the 'goodness of their hearts' for granted either.