The author probably only finds confinement-as-punishment morally unacceptable because he believes that just punishment will be meted out in the afterlife anyway. If you take away the assumption of religion, there's really no argument left.
No proper Catholic would think, "We don't need to punish people now because they'll get theirs in the afterlife". That is absolutely not a Catholic view for a number of reasons.
"But we are not merely allowing the abomination of the prison. We are promoting it (and in popular culture and politics, romanticizing it). And in the case of the very limited number of those with deeply disordered desires, we are taking the tremendously difficult task of healing, a task best addressed locally, in families, neighborhoods, and communities, and elevating it the level of the state, where rationalized violence compounds and conceals the real harm that must be addressed."