I'm usually good at playing devils advocate and look at the other point of view when pondering about such things, but I really can't think of any good reason why if the enemy were the only ones remaining that I should allow them to remain after what they'd done.
A good reasons for not mindlessly nuking and murdering thousands of people? Well, let's see:
Realizing that humanity is all on the same "team" would help a lot. We're all in this together. People that cause division and constantly label other humans the "enemy" are usually either missing something, or politicians.