Punishment would be cruel, in the absence of free will. You could say 'If we let him go, he might rob another bank', so he needs to be locked up to prevent that.
That's a reasonable argument, but to say 'We need to punish him for what he did' makes no sense if what he did wasn't up to him.
It's like somebody waking up from a coma with no memory of the last few years; only to find he committed a crime and is now in jail. Sure he's capable of the crime, we know that because he did it; but if he doesn't remember making the decision, then how are you justified in punishing him for it?
I'm not arguing he be released, just that his incarceration be reframed as preventative, rather than punitive.