Most, if not all, of the 13,000 Americans that Lincoln imprisoned were in Union states, under Union control. Some were Union state legislators; Union state newspaper editors whose only crimes were to criticize Lincoln. The newspaper editors did not fire on federal troops.
President Lincoln suspended habeas corpus for United States citizens.
At some point you need to come to grips with what he did.
With all these conspiracy theories floating around, consider this one: Maybe Jefferson Davis and the other secessionists were agents (paid or not) of the abolitionists or the Northern industrialists. Things happened to slavery and the South that wouldn't have happened if they'd only stayed with the union. Maybe that was what key secessionists were secretly working for. It's not as crazy as some things people say on line.