"...if we understand that there are good evolutionary reasons for our wanting people to suffer when they have done direct or indirect harm to us, then we can account for our strong feelings about the appropriateness of retribution without presuming they are a guide to moral truth.... We may be able to recognize our retributivist feelings as a deep and important aspect of our character - and take them seriously to that extent - without endorsing them as a guide to truth, and start rethinking our attitudes toward punishment on that basis."  ---Janet Radcliffe Richards, Human Nature After Darwin, p. 210

Naturalism encourages an empirically-based, comprehensive understanding of the causes of criminality. Knowing the full causal story behind the offender allows us to design effective interventions to prevent crime, abuse, and dysfunction. Seeing that criminals are not self-made undercuts retributive attitudes favoring the death penalty and punitive prison conditions. Realizing that but for the luck of circumstances, any of us could be standing in the criminal’s shoes generates compassion for offenders as well as for victims.

With a naturalistic view of ourselves, we don't have the sort of ultimate responsibility that has traditionally justified retributive punishment.  Naturalism therefore implies a radical revision of our criminal justice system, moving away from unnecessarily harsh, retributively motivated sanctions (e.g., the death penalty, abuse of prisoners), toward crime prevention, rehabilitation, restitution, and minimally punitive deterrence and incapacitation.