The ONLY attempt at prosecution was to bring Merryman before the CIVILIAN COURTS.
All charges against Merryman were dropped.
The stated Government purpose of the Government troops was to retake all U.S. Government facilities in the South, not to protect Washington, D.C. from a non-existent attack. If those troops were to protect Washington, D.C., then what troops were going to invade the South and provoke the attack on Washington, D.C.?
The truth is painfully clear. Those troops were for, and were used for, the purpose of subjugating the state of Maryland to prevent the possibility of its secession.
But none of this diversion changes the Merryman case.
Merryman was NOT, as you so ineptly argued, subject to the Laws of War.
As the Court said in Ex Parte Milligan,
It follows, from what has been said on this subject, that there are occasions when martial rule can be properly applied. If, in foreign invasion or civil war, the courts are actually closed, and it is impossible to administer criminal justice according to law, then, on the theatre of active military operations, where war really prevails, there is a necessity to furnish a substitute for the civil authority, thus overthrown, to preserve the safety of the army and society; and as no power is left but the military, it is allowed to govern by martial rule until the laws can have their free course. As necessity creates the rule, so it limits its duration; for, if this government is continued after the courts are reinstated, it is a gross usurpation of power. Martial rule can never exist where the courts are open, and in the proper and unobstructed exercise of their jurisdiction. It is also confined to the locality of actual war. Because, during the late Rebellion it could have been enforced in Virginia, where the national authority was overturned and the courts driven out, it does not follow that it should obtain in Indiana, where that authority was never disputed, and justice was always administered. And so in the case of a foreign invasion, martial rule may become a necessity in one state, when, in another, it would be 'mere lawless violence.'
And so it is that you must defend the "lawless violence" of the Great Usurper with the same mindset as those who argued to the Court that the Milligan case should be dismissed because, in the absence of evidence having been provided to the contrary, the Court should assume that Milligan had been hanged pursuant to the sentence of the lower court. The Supreme Court did not buy that insane argument, and nobody will buy your insane argument.
But it is said that this case is ended, as the presumption is, that Milligan was hanged in pursuance of the order of the President. Although we have no judicial information on the subject, yet the inference is that he is alive; for otherwise learned counsel would not appear for him and urge this court to decide his case. It can never be in this country of written constitution and laws, with a judicial department to interpret them, that any chief magistrate would be so far forgetful of his duty, as to order the execution of a man who denied the jurisdiction that tried and convicted him; after his case was before Federal judges with power to decide it, who, being unable to agree on the grave questions involved, had, according to known law, sent it to the Supreme Court of the United States for decision. But even the suggestion is injurious to the Executive, and we dismiss it from further consideration.
As may be readily observed, desperation does not add substance to an insane argument.
He was charged with treason. If he was held as a prisoner of war, I don't believe he would have been tried at all.
"All charges against Merryman were dropped."
Taney stymied any trials for in excess of a year. By that time, the immediate disloyalty crisis in Maryland had passed. Eventually Merryman was released on bail, and if I am not mistaken, he defected south.
With respect to your lengthly passage from Ex parte Milligan, the Court apparently had "second thoughts" in Ex parte Quirin:
"Petitioners, and especially petitioner Haupt, stressed the pronouncement of this Court in the Milligan case ... that the law of war 'can never be applied to citizens and states which have upheld the authority of the government, and where the courts are open and their process unobstructed.' ... We construe the Court's statement as to the inapplicability of the law of war to Milligan's case as having particular reference to the facts before it. From them the Court concluded that Milligan, not being a part of or associated with armed forces of the enemy, was a non-belligerent, not subject to the law of war save as ... martial law might be constitutionally established. The Court's opinion is inapplicable to the case presented presented by the present record. We have no occasion to define with meticulous care the ultimate boundaries of the jurisdiction of military tribunals to try persons according to the law of war. It is enough that petitioners here, upon the conceded facts, were plainly within those boundaries...." (Rehnquist, Pg 137).
Merryman's situation, as a member and officer of the disloyal Maryland militia engaged in sabotage, is much more like that of Quirin than than Milligan.
I find it interesting, though, that you make the same case for Merryman (not being subject to the laws of war) that the American-born nazi saboteur Haupt made for himself. John Merryman most certainly could have been tried by a military tribunal, if that is what the government had wished to do.