A hundred and forty years later we are having debates about prisoner abuse centered on allegations that a guard peed on someone's holy book... by accident.
One does not need to read wartime propaganda to get a full indictment of the prison camps. Each side indicted itself, in terms no propagandist could make much more bitter. A Confederate surgeon, completing an inspection of Andersonville, reported to his superiors at Richmond that more than 10,000 prisoners had died in seven months--nearly on third of the entire number confined there. More than 5,000 were seriously ill. Diarrhea, dysentery, scurvy, and hospital gangrene were the chief complaints, and there were from 90 to 130 deaths every day. He found 30,000 men jammed together on twenty-seven acres of land, "with little or no attention to hygeine, with festering masses of filth at the very doors of their rude dens and tents." A little stream flowed through the camp, and about it the surgeon found "a filthy quagmire" which was so infamous that a man who got a slight scratch on his skin, or even an insect bite, was likely to die of blood poisoning. [...]
Thus in the South. In the North, an army surgeon inspected the camp for Rebel prisoners at Elmira, New York, and said that the 8,347 prisoners there exhibted 2,000 cases of scurvy. He asserted that at the current death rates "the entire command will be admitted to hospital in less than a year and 36 per cent die." Like Andersonville, the Elmira camp contained a stream, which had formed a dreadful scummy pond--"a festering mass of corruption, impregnating the entire atmosphere of the camp with the pestilential odors... the vaults give off their sickly odors, and the hospitals are crowded with victims for the grave." The camp surgeon had made repeated complaints but he could get no one in authority to pay any attention to them, and his requisitions for medicines had been entirely ignored.
Let's see if we can gain a little more perspective from Catton. Here he is discussing the war as it was fought in the Shenandoah Valley.
In modern terms, the Confederacy had organized a resistance movement in territory occupied by the hated Yankees; had organized it, and then had seen it get badly out of hand. The Valley was full of men who were Confederate soldiers by fits and starts--loosely organized and loosely controlled, most of them, innocent civilians six days a week and hell-roaring raiders the seventh day. They owned horses, weapons and sometimes uniforms, which they carefully hid when they were not actually using them. Called together at intervals by their leaders, they would swoop down on outposts and picket lines, knock off wagon trains or supply depots, burn culverts and bridges behind the Federal front and waylay any couriers, scouts, or other detached persons they could find. They compelled Union commanders to make heavy detachments to guard supply lines and depots, thus reducing the number of soldiers available for service in battle. To a certain extent they unintentionally compensated for this by reducing straggling in the Federal ranks, for the Northern soldier was firmly convinced that guerillas took no prisoners and that to be caught by them was to get a slit throat.
The quality of these guerilla bands varied greatly. At the top was John S. Mosby's: courageous soldiers led by a minor genius, highly effective in partisan warfare. Most of the groups, however, were about one degree better than plain outlaws, living for loot and excitement, doing no actual fighting if they could help it, and offering a secure refuge to any number of Confederate deserters and draft evaders. The Confederate cavalry leader, General Thomas L. Rosser, called them "a nuisance and an evil to the service," declaring:
"Without discipline, order or organization, they roam broadcast over the country, a band of thieves, stealing, pillaging, plundering and doing every manner of mischief and crime. They are a terror to the citizens and an injury to the cause. They never fight; can't be made to fight. Their leaders are generally brave, but few of the men are good soldiers."
In short, these men were not looked on by either side as being regular army soldiers. The Union reaction to these men was harsh.
Just in case that's not clear, the word he used was "interment" not "internment", in other words, burial. He was telling his men, don't bring me any live guerillas. This was the custom of the time, and was still the custom in WWII. Men not serving as part of a regular army were not protected by wartime conventions. They were subject to be hanged or shot, as the mood suited the capturing parties. The reason for this was very simple. By not operating openly, they had what was considered an unfair advantage over troops who did. In addition, by posing as civilians they were taking advantage of the protection assumed for civilians during wartime. They were also blurring the distinction between civilian and soldier, and exposing civilians to reprisals as a consequence. The principle by which they were executed when caught was: men who do not fight by the rules of war may not appeal to the rules of war for protection.
"[M]ost Federal generals considered guerillas as mere bushwhackers, candidates for the noose or the firing squad. An exception was generally (though by no means always) made in the case of Mosby's men, who were recognized as being more or less regular soldiers, but the attitude toward the rest was summed up by a Union general along the upper Potomac, who said: "I have instructed my command not to bring any of them to my headquarters except for interment."
To the best of my knowledge, every single one of the men interned at Guantanamo was wearing civilian clothing when captured. By long-standing rules of war, we could have executed them on the spot, and we would have been justified in doing so. Having chosen to treat them as prisoners of war instead, we are treating them in a far more humane manner than has been customary for even legitimate prisoners of war. None have died of disease or ill treatment. They are given excellent medical care, and plenty of food. Some of them have been interrogated, but only in ways that would have made Torquemada snort with derision.
A knowledge of history teaches us that war is hell on earth. It should not be undertaken lightly, but when it must be undertaken, it must be fought to win. Victory is not achieved by gentle handling of the enemy. The prisoner of war camps in the Civil War are not a model we want to emulate. According to Catton they were not part of a deliberate policy of cruelty, but a result of the fact that "men were clumsy and the times were still rude." Most soldiers during that time died from the same sort of disease and malnourishment that was killing the POWs, so it was no surprise that soldiers of the enemy received worse treatment. Giving terrorists--men who wage war by murdering civilians--enough nourishment and medical care to keep them alive until such time as they can be executed, is more than sufficient for humane treatment.