I bought Chrono Trigger on the release day back in '95, and have played all the way through it about 12 times. I have only refused Magus' company once, and all 11 other times he has never done anything harmful to my party. The only difference is, if you don't take Magus, Frog gets to become human again at the end of the game. If you take Magus, Frog stays in frog form. Trust me, nothing bad happens.