Principles and aspirations often clash with the real world.
You never addressed the point of amnesty. Why did the President grant amnesty?
It doesn't matter why the President granted amnesty. What matters is the principle itself. If we accept, as the founders did, that the right to self-government is a natural right, or a god-given right if you're a religious person, then it doesn't matter what a king, president, prime minister, chief of police, or anyone else says. Our nation was founded on the belief in the natural, or god-given, right to self-government.
My point, all along, has been that it's hypocritical that our government, which was formed under the idea of a natural right to self-government, denied that natural right when a group of states wanted to break away from us. Now, you can say that treason is in the eye of the beholder, and you'd be right because we can all have our own idea about what constitutes treason, but you can hardly deny that the principle of self-government was denied to the Confederacy by the U.S. government under Abraham Lincoln.
If you accept the natural right to self-government, then you have no reason to brand the Confederates traitors. If you don't accept the natural right to self-government then I'd say you have to brand the Colonists as traitors. To say that the Colonists weren't traitors, but that the Confederates were, is gross hypocrisy in my opinion.