For one thing, the unanimous Supreme Court that decided the Milligan case included five (out of nine Justices) who were Lincoln appointees, including Justice David Davis (an Illinoisian and one of Honest Abe's oldest and closest friends/supporters), who wrote the opinion of the Court. By embracing their opinion, you are in fact paying President Lincoln a high compliment for his judicial appointments.
The main issue in Milligan concerned the scope of military tribunal authority during an armed rebellion/war, and more specifically whether an enemy operative who is a citizen of the United States could Constitutionally be treated as a prisoner of war or instead should be given the full compliments of judicial rights of a U.S. citizen regardless of his treasonous activities.
As usual, the extensive vaguaries of the U.S. Constitution provided fertile ground for argument by all parties and interested jurists. The case was argued on behalf of Milligan by none other than David Dudley Field, the learned brother of (my all-time favorite) Justice Stephen J. Field (another of the Lincoln appointees who joined in the Court's opinion). All of the quotes in the official report of the Milligan case that you mistakenly attribute to Justice Davis (in Posts #55, #57, and #59 above) were in fact part of David Dudley Field's arguments (excepting your last one in Post #57 -- "The Constitution of the United States is a law for rulers and people, equally in war and in peace..." -- with which Lincoln would have certainly agreed).
Of course, Lincoln wasn't available to voice his approval of his Court's Milligan decision, having been done in by the type of cowardly act by a traitorous U.S. citizen that Milligan was apparently planning when he was apprehended.
Milligan is indeed an interesting case -- it just doesn't say what you seem to think it does. It didn't reject the notion that the President has the power to suspend habeas corpus or to declare and enforce martial law in states in rebellion or in which hostilities have rendered the federal courts inoperable. Rather, it simply held that where the federal courts are operable, all persons are entitled to trial by jury, even if their admitted purpose is to violently overthrow the government and they are in the process of doing so when they are arrested.
Interestingly, three of the Associate Justices joined Chief Justice Chase in a separate concurring opinion in which they rejected the general conclusion of the Court but determined that in the case at bar, Congress had not exercised its authority to provide for military trials of traitors in Indiana.
In summary, no reasonably skilled jurist would interpret Milligan as any kind of a moral indictment of President Lincoln.
You also seem to have run your critics off!
Cheers,
Richard F.