The original purpose was similar to the purpose it has today. I think the words criminal justice system speaks for itself. A criminal justice system is made for criminal justice. Criminals are people who violate a systems laws and regulations. This harms not only others but a created system of regulation itself. There has to be justice for criminals- this really benefits them in the end.
The goal was to defeat the rebellion by blockading southern ports and controlling the Mississippi river. This would cut off and isolate the south from the outside world.