It sounds like you want to add in some house rules to represent a form of "Humanity loss" (similar to White Wolf games, for example). Aspect change is definitely the way to go; if you want "mechanics" for it, why not use the aspect darkening guidelines that go along with Lawbreaker powers as a baseline?
Don't actually force the purchase of a stunt or power (or if you do, make it a -0 mortal stunt as a placeholder, so no refresh loss of bonuses), but keep track of "alignment infractions", and slowly darken aspects as they build up. Don't apply this to characters who commit crimes that are in-line with their existing aspects -- for example, a character with the aspect "The gene pool is gettin' a bit dirty -- call me the pool man!" who kills a rapist is acting to his aspects and shouldn't need to do anything. And, of course, if at some point the aspect become "dark enough" to reflect that that sort of action is in line withe his "alignment", stop tracking that particular type of crime...