Witches

The natural disaster stopped after the witch was massacred. Doesn't it mean the world itself suffering when witches roaming around? While genocide is certainly wrongful action, the witches can't stop their way of living because that is their instinct. So the offer to let them live, but ask them to do nothing against the nature would be difficult. Its like asking lion not to eat meat. So there's no way but to vanished them.
Or am I missing something?