We did a slightly similar thing in our old TSR Marvel game: My hero (a mutant) saved a radical anti-mutant villain from a certain death against even his better judgment. I believe my position was that his commitment to protecting people was stronger than his disgust at the guy's villainy. Team mates even told me I should have let him fry.
Of course, the resolution wasn't so cheery for my hero: Every time this guy did something against mutants it was a knife in the back. Eventually the GM felt sorry for me and my character, and had Wolverine give him a little "You're a good guy, you couldn't let die, even if he did deserve it. It's why you put on that uniform." type of pep talk, and then gave me a little XP bump whenever I role played dealing with the guys actions. (Side effect was everyone trying to save badguys).
Ah, Role-playing!
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"Yes, it's the Apocalypse alright. I always thought I'd have a hand in it"
Professor Farnsworth