"Evil" is subjective. Atrocious things are done to and by the human race in the name of "good", and they are taken that way because people don't see them as "evil".
I'd have to ask a question that I've asked long ago, was Neo wrong for going through the door the Architect told him would bring about the destruction of the human race, just because he thought there was another way?
Hindsight is 20/20, as they say. Looking back on it from our perspective, it's easy to say that Neo was right when he chose that door. But if his actions really had brought about the end of humanity (from both the destruction of Zion and then the crash of the Matrix)...well then, that would have been the wrong choice.
Illyria