In criminal justice most of our system doesn't deal with morality either.As for criminal justice, the biblical principle is basically the inverse of the Golden Rule. It is done to the criminal as he did (or sought to do) to his victim. The punishments dealing with religious crimes are a different issue and were both in place and punished for various, often symbolic, reasons that are not directly related to morality and had to do only with the nation of Israel within their peculiar relationship with God.
One article I read was dealing with punishment in different ways.
With utilitarianism the example was given of a law enforcement framing an innocent man and executing him. In terms of utilitarianism this would be just (as long as the people believe the man was guilty then it would serve to prevent further crime).
With moral punishment the example was given of three people knowing for a fact a man committed a heinous crime. If morality were the only component those three should lynch the man without wasting time for a trial (where he could be found innocent).
But the conclusion was that "justice" (secularly) is an amalgamation of these elements.
It is interesting to consider.