Yes. He did kill a ton of people. Yes he did try to "destroy" the world.
But in the end he felt empathy and remorse. Yes he tried to cover it with "this world is black hell" but that doesn't mean he isn't sorry for what happened.
Theres a reason courts take remorse into account when giving judgements. Those who are found to be happy, willing even to admit to a murder should be punished to the fullest extent of the law. Those who are regretful, and distraught will still be punished, but the severity will be much different.
This is a Manga. It's based around a character who wants everyone to be happy and peaceful. He is not the Eye for an Eye type. He is the forgiving type.