Sure they do. The Laws of War applied when Lee rolled into Sharpsburg in 1862 and through the state on the way to defeat at Gettysburg in 1863. Just as they did in 1861.
You can chant your mantra over and over again - it's not going to make your story any more thruthful.
You can chant your Blue State radical liberal judicial revisionism all you want, but the actual law, and the actual judicial opinion rendered in the case will continue to say you are full of crap. The opinion is quite specific in holding that the rules of war did not apply. Not even the government tried to maintain that line of B.S.
The chief justice then proceeded as follows:'I ordered this attachment yesterday, because, upon the face of the return, the detention of the prisoner was unlawful, upon the grounds:
1. That the president, under the constitution of the United States, cannot suspend the privilege of the writ of habeas corpus, nor authorize a military officer to do it.
2. A military officer has no right to arrest and detain a person not subject to the rules and articles of war, for an offence against the laws of the United States, except in aid of the judicial authority, and subject to its control; and if the party be arrested by the military, it is the duty of the officer to deliver him over immediately to the civil authority, to be dealt with according to law. It is, therefore, very clear that John Merryman, the petitioner, is entitled to be set at liberty and discharged immediately from imprisonment. I forbore yesterday to state orally the provisions of the consitution of the United States, which make those principles the fundamental law of the Union, because an oral statement might be misunderstood in some portions of it, and I shall therefore put my opinion in writing, and file it in the office of the clerk of the circuit court, in the course of this week.'