The problem is the guarantees given by the Constitution to the States; like the Republican form of government -- is the power of assigning governorship a power delegated the FedGove by the Constitution? That they 'rebelled' is immaterial in that argument; much like prison-rape is not a-ok because the inmates are in prison; this because being convicted, even of the most heinous crimes, does not invalidate unalienable rights [else they are not unalienable].
In short: does another's wrongdoing absolve us of abiding by [the 'right' of] a right/wrong ethos?
And what's your feelings towards those southerners, chiefly in the Appalachian regions of west Virginia and east Tennessee, who remained loyal to the union?
I have little opinion on them, either way.
Why do you think they remained loyal?
For this discussion, I actually don't care; the problems I present are discretely separate from such questions, and therefore those questions are irrelevant distractions.
Whatever "unconstitutional" actions Lincoln foisted on the southern states, they brought it all on themselves. Ditto for northern Copperheads who found themselves jailed or removed for seditious actions during the war. I find it risable that you're outraged about Lincoln appointing governors (oh, the horror!!! ) more than some states retaining the institution of slavery.