Magus doesn't necessarily view himself as a bad guy, no, but certainly not a good guy. He recognized that the things he did as the Fiendlord were evil, and the experience was obviously bad enough for him to refer to it as "THE DARKNESS", but he was also consumed by revenge so much that he didn't do the "right" things when the options were there. The dude regretted focusing on killing Lavos more than grabbing Schala and some choice Zealians, getting in the magic getaway buggy and blowing that popsicle stand.
I still think of him talking about how to bring back Crono as his first nice thing to do, especially since he does it even if you kill him, but more importantly it gave a believable reason for him to be allowed in the party in the first place. If he just tagged along to fight Lavos without providing anything else, they wouldn't have let him in the Epoch, many gamers would think. Even if you kill him, it gives you a clue where to go next.
AS FOR FROG'S MOTIVATION... he's too heroic to ditch the gang mid-adventure even if he becomes human again. And through the course of the game, the people of his time accept him as a frog anyway. He's about proving he has his own will, and I think part of that will is sticking around with Crono and co. to save the world. I mean, he sticks around after you recruit Magus, that's gotta say something.
