If I understand correctly you're saying that people having a lack of free will cuts out the legs from the rationale for punishing people if they have not chosen to do something wrong. The five purposes for punishment as I understand it are generally deterrence, incapacitation, rehabilitation, retribution and restitution.

Retribution and restitution as punishments don't seem justifiable without free will or the ability to have mens rea, but punishments for the sake of deterrence, incapacitation and rehabilitation still seem reasonable if free will is assumed to not exist. For example incapacitating someone who is clinically insane and dangerous is already considered reasonable, and not on the grounds that they have using free will chosen to be insane.