I don't think that Michael thought that the Mafia was evil so much as it was backward and unproductive. I think that he probably thought similarly about the other trappings of being a Corleones, such as Catholicism and Italian culture, and also family (with a small f). It was Michael's bad luck that Vito got shot when he did: Michael was a grown man, yet hadn't really established other ties yet, so he had to get involved. If Vito had gotten shot five years later, Michael would have been established in his own suburban or college town life, with a couple of Protestant children, and he wouldn't have been expected to make any kind of contribution to the ensuing fight.