Leonard’s motives may have been malicious. But not only has Luther been biased and way out of line, he demanded on leading and lead in the worse way possible. He suffocated Vanya when she was in tears saying that she was sorry. Then, when the person that Vanya hurt, Allison, tried to go visit her. He stopped her. He held a grudge that he had no place holding, for the damage was not inflicted on him. Vanya was fine but solitary confinement started her rage. She killed Leonard because he was a bad influence. She ended the world because everyone else in her family was wrong. Which was incorrect, but that was all she knew because she was confined instead of trying to reason with her powers. He treated her as only a threat and not a human. Literally referring to her as the bomb and offering to let her die in the apocalypse when she was unconscious.