Suggest you go back and take another look at how those freedom-loving Founders treated those of their fellow citizens who disagreed with them on whether America should split with Britain.
The Tories were treated MUCH worse than rebels were during the War Between the States and its aftermath.
http://threerivershms.com/loyalistspersecution.htm
That's how the Founders themselves treated those who fought them in a civil war.
The Founders fought a War of Independence, a war of secession from the British Empire. Your claim regarding the Tories is quite debatable, but also beside the point. You are talking about a period before the Constitution by which the states had created a federal republic that was to be bound by certain rules. In fact, after the founding in the situation most analogous to part of the Lincoln dictatorship, the Federalists’ Alien & Sedition Act, was repudiated by most of the Founding generation, and its repeal was forced in 1802.