"it is the Right of the People to alter or to abolish it, and to institute new Government, laying its foundation on such principles and organizing its powers in such form, as to them shall seem most likely to effect their Safety and Happiness."
You did not address the fact that there is no enumerated prohibition against secession and therefore it is a 10th amendment right held by the states.
The colonists openly rebelled without pretense or deceit.
I have already noted that the southern states seceded quite openly and by Democratic means.
"Lincoln was certainly equally harsh..." - I categorically reject that premise. Lincoln's response to the south was reactionary and slow to get up to speed but he did not treat the rebels as harshly as the Brits treated the colonists.
"If a pigeon attempted to fly the length of the Shenandoah Valley he would have to pack his own rations"… General Phil Sheridan in his report describing the devastation he wrought in the Shenandoah Valley. Sherman's march to the sea was worse.
The main difference is that they [West Virginia] did not attempt unilateral secession like the confeds.
Of course they did, they conducted the secession from Virginia without reference to the will of the people of the whole state, protected by force of arms of Union troops. When the southern states seceded they submitted the issue to all the people of all of the southern states respectively.
The secession of West Virginia stands in hypocritical contradistinction to the war of Northern aggression conducted against the South for doing the very same thing.
