That court’s ruling was indeed correct, in the sense that it agreed with me: constitutional under the raising-armies and the necessary-and-proper clauses.
I was responding initially to your statement that Lincoln acted extra-constitutionally, which seemed to me to imply that it was well-known at the time that only Congress could suspend habeas. The reality is that at that time, it was uncertain which branch of government could suspend habeas, since there was not any case-law on the issue prior to the Civil War. So, it was not so cut-and-dried at that time that Lincoln was acting “extra-constitutionally.” The issue was an open one.
As a result of Lincoln’s actions, there was a significant court case which held that only Congress could suspend habeas: Ex parte Merryman, a decision by Chief Justice Taney, holding that only Congress can suspend. However, that was a circuit court decision, not a decision of the Supreme Court.
Chief Justice Rehnquist has written about this issue, in a book on Lincoln’s position. He seemed to be sympathetic to Lincoln’s argument that the power to suspend habeas was part of the President’s war-making powers during a war.