If Napolitano claims that anyone other than the confederates committed treason then he is committing the equivalent of journalistic malpractice. He (and you) should be ashamed.
Watched the Judge's comments. He seems to be under the peculiar impression that treason against the United States consists of levying war against any one of them.
Which would of course make Andrew Jackson guilty of treason, as he prepared to launch war against SC when it threatened secession.
It also would make it quite impossible for the federal government to fulfill its obligation to guarantee every state a republican form of government, since any state taken over by an oligarchy or dictatorship could simply claim it would be treason to use force to remove that unconstitutional government.
The judge also does not appear to recognize that most of the violations of liberty by Lincoln were also put in place by Davis, often first by him.
The basic problem is that the Constitution is very elastic, but it is not infinitely elastic. It was not designed by the Founders to be able to stretch across and enclose a great civil war. Go back sometime and read how the Founders themselves handled their own opponents in the civil war within the Revolution. The Loyalists were handled far more harshly than secessionists and their sympathizers during and after the WBTS.
What is astonishing is not that constitutional liberties took a major hit during the War. It's that they were respected as much as they were, and that they were restored at the end of the war, with remarkably little vengeance taken on the defeated. At least if you compare our civil war to any other great civil war in history rather than some delusional war somewhere fought without violating anyone's human rights.