Quote Originally Posted by The Man View Post
He wants to kill Lavos because, if unmolested, will result in the destruction of humanity. I'd say that's a rather large selfless desire. I always interpreted his apparent disregard for the lives of others as a façade maintained to win the trust of the Mystics; whether the fact that he is willing to go to such extents to destroy Lavos makes him evil is a philosophical question raised but ultimately unanswered by the game.
I haven't been around lately, so I'm late to respond. But this pretty much sums up why Magus is really "good underneath it all". He's puts on a selfish/cold façade, mostly for the reasons you specified, but probably also because of how he grew up as well [dealing with Queen Zeal after she was corrupted and their abuse of his sister and her powers].

Yes he wants to kill Lavos for revenge, but the basis for that revenge is more-or-less based on his compassion for others. It's also quite clear that he cared/still cares for Schala very much as Kawaii Ryűkishi pointed out.