You make a valid point. Just war theory involves two logically separate components, jus in bello and jus ad bellum. The first governs conduct of soldiers during wartime, and the second governs acceptable reasons for engaging in warfare. They are logically independent in the sense that a soldier fighting in a war that was illegitimate in its conception still can fight in a manner that is honorable and legitimate. That soldier is still entitled to the protections of the laws of war (such as those codified in the Geneva Conventions, for instance).
Conversely, a soldier fighting for a country that was legitimately justified in going to war can commit war crimes. The question of whether Sherman committed war crimes, then, is completely independent of any justification for fighting the war. The laws of war are indeed fairly clear - it is impermissible to intentionally target civilians. Sherman’s army clearly did target civilians intentionally. The only question for Sherman’s personal responsibility is whether he specifically ordered such targeting. It certainly seems to me that he did not specifically order civilians to be targeted, but that he must nonetheless be held responsible for the actions of his men. He failed to do enough to maintain discipline to prevent widespread targeting of civilians and he should have realized that his plan for the “March to the Sea” had great probability of resulting in civilian casualties.
There is also another question -- could Sherman have stopped his troops from burning houses? In the case of the wholesale burning of Columbia, South Carolina, he did not stop his troops. Here is his testimony before an 1873 commission:
Q. -- You testified, a little while ago, that it was very likely they [Sherman's own men] might burn Columbia, and you permitted them, or your officers did -- permitted them to go about the town?
A. -- I could have had them stay in the ranks, but I would not have done it, under the circumstances, to save Columbia.
Q. -- Although you knew they were likely to burn Columbia, you would not restrain them to their ranks, even to save it?
A. -- No, Sir. I would not have done such harshness to my soldiers to save the whole town. They were men, and I was not going to treat them like slaves. ...
I'm returning to what you posted above because Sherman did, in fact, order the targeting of civilians and their houses and cities on occasion. I cite the following from the Official Records of the war, that massive collection of cables, orders, and reports issued during the war.
General Sherman to General Schofield, August 1, 1864: "You may fire from ten to fifteen shots from every gun you have in position into Atlanta that will reach any of its house. ... Thomas and Howard will do the same."
General Sherman to General Watkins, Calhoun, Ga., October 29, 1864: "Cannot you send over about Fairmount and Adairsville, burn about ten or twelve houses of known secessionists, kill a few at random, and let them know it will be repeated every time a train is fired on from Reseca to Kingston?
General Sherman to General George H. Thomas, November 11, 1864: "… Last night we burned Rome, and in two or more days will burn Atlanta ..."
General William D. Whipple to General D. S. Stanley, November 13, 1864: "General Sherman left Kingston yesterday morning; camped at Allatoona last night; will probably reach Atlanta to-morrow, whence he starts on his trip south. He has already burnt Rome, and says he is going to burn Atlanta and other towns south."
I also found the following in the History of South Carolina:
Sherman is reported to have said the following in Salem, Illinois, in July 1865 about a change in policy he made on his march to the sea. "Therefore, I resolved in a moment to stop the game of guarding their cities and to destroy their cities."