Enhanced Punishment is Death
In seeking to find punishment for criminals, the above article expresses an heretical view held by the Valentinians, who were Gnostic in nature. Their leader, Valentinus, lived around the year 150. The core of his system of thought is that we are chained to this physical world, and Christ came to free us from that so we could be solely spiritual. In his dualist idea of the world matter is evil, spirit is good, and through a special knowlege we can be freed from matter.
In the article, the special knowledge is Science, and it might one day free prisoners from their bodies by uploading their consciousness to computers. The writer of the article suggests we do this so that we might punish criminals for much longer lengths of time than a body can survive.
The separation of body and soul to better punish the soul is based in heresy because Catholics believe the body and soul together make up the human. Separation of body and soul is death. Therefore, an uploaded mind is just a simulation of the real deal, because it is missing its body. Running simulations does not enforce justice. Similar to running simulations of a person to punish them would be to take their dead body and torture it to punish the person. The person is dead, body and soul have been sundered, so beating up upon a dead body does no punishment just as beating up a computer simulation does no punishment.
In our world often follow this Valentinian ideal and think it is the mind that makes the person. Our Catholic faith has been fighting this for over 1850 years, and sees the body as no less important in the make up of a person than the mind.