I usually save Magus. Though I disagree with you on how he thinks.

Magus isn't trying to write his wrongs, he isn't trying to help people. His sole reason for wanting Lavos gone is revenge. He doesn't seem to care how many people he kills to keep his position in the Mystics, just so long as he can kill Lavos.

Mind you, I do agree he is not inherently evil, as he offers to help Crono, but as for his quest to kill Lavos, thats just doing the right things for the wrong reasons.