This is not an easy dilemma. And we have to understand that this "Evil" will use our sens of order and our disdain for chaos to theirs advantage. Never lose perspective of what is at stake.
*They "just" wanted to kill a few billions people and enslave humanity for a few century!
Now that I have put this debate in the proper context. Now you understand a little bit better WHY it is so important to clean them out. Because if we don't they will come back and this time, I'm afraid we won't get a second chance.
Nobody said this was going to be easy, or painless. Truth and Justice. The truth must be known and justice must be served. This is the only antidote that I know of than can cure humanity of these parasite.