The recent "War on Terrorism" has generated some perplexing legal problems with regard to how a nation state, in particular the U.S., may treat "unlawful combatants," i.e., persons who are members of a non-state terrorist group. As such, they are said not to enjoy the protections of the Third Geneva Convention. Furthermore, the U.S. government asserts the right to detain them until the end of hostilities; however, when such persons are U.S. citizens, their right to petition for habeas corpus stands against the government's claim to detain them for the duration of hostilities. Clear and uncomplicated rulings on these issues seem remote, and it is doubtful that the law governing such cases will be settled anytime soon.
The difficulty is not without precedent, though, as is demonstrated in Burrus M. Carnahan's recent book Lincoln on Trial. Carnahan amply illustrates the legal, political, and moral difficulties that Lincoln and the military forces of the Union had in dealing with Confederate rebels. As with the current conflict, the legal treatment of Confederate rebels was complex and at times contradictory.
At the start of the war, Lincoln took pains to do nothing that would bestow sovereign status on the seceded states. This was far from simple. The first challenge was to maintain a blockade of Southern ports. To be effective, the blockade would require Union ships to search and seize ships and their cargoes outside of the territorial waters of the U.S. Under international law, this would be permitted only if the South were recognized as a sovereign state.
Similarly, the right of the Union armies to appropriate supplies from non-combatant Southerners would exist only if the population was deemed an alien population, not protected by the Constitution. Furthermore, captured Union soldiers could not be exchanged for Confederate soldiers unless all were officially classified as prisoners of war. Lincoln's response to these dilemmas was to gradually act as though the Confederacy was a sovereign state.
Carnahan's book is primarily a litany of ostensible violations of the rights of Southern non-combatants. Through out, Carnahan argues that Lincoln largely allowed his generals to interpret and abide by rules of engagement for Union troops developed and outlined by Francis Lieber in the Lieber Code; however, when specific controversial acts that did not seem justified by military necessity were brought to his attention, Lincoln commonly intervened without ever establishing broader executive orders to prevent future abuses.
The final verdict appears to be that Lincoln expected his generals to interpret and abide by a code of conduct that might justify significant attrocities under strained interpretations, but would not, himself, reach those interpretations. In all, Lincoln appears to have approached the problem pragmatically, seeking to minimize damage to the South, without compromising the aims of the war.