I think you confuse allegiance to Lincoln with allegiance to the Constitution. At West Point during that era they used Joseph Story’s Commentary on the Constitution to teach government. Story, of Massachusetts, taught what most Americans of that time believed, that secession was a right held by the States. Unsurprising since the New England states had flirted with secession in 1814 with the Hartford Convention.
Moreover the authority of States to overrule the national government was a belief expressed by both Jefferson and Madison in the Virginia and Kentucky Resolves which they authored in 1798. Those Resolves are a basis of the States Rights doctrine which was espoused by the Confederacy.
In a similar vein Jefferson Davis was never brought to trial for treason despite his repeated requests that he either be charged or released. Davis was certain that he had broken no law and it appears to be a belief shared by his captors who refused to charge him.
The belief in an all powerful national government is something that is taken for granted only after Lincoln. It was an era of triumphant nationalism and not just in America. Lincoln crushed the South’s attempt to leave the union. The German states unified. Italy unified.
Justice Story did not believe that secession was a right. He called it a "baneful practice ... which is subversive of all the principles of order and regular government, and which leads directly to public convulsions, and the ruin of republican institutions" Source. In his Commentaries Justice Story cited Jackson's message about secession, and by all indications Story agreed with Jackson's unionist views.
You may have Justice Story confused with William Rawle. Rawle's book was used for perhaps one year or at most two at West Point, for want of a better text. It may have been taught while Davis, Lee, and Johnson were at West Point, or perhaps not -- Davis didn't remember using the book. Most serious scholars agree that the brief period when Rawle was used as a text did not account for the widespread later acceptance of secession as constitutional.
Moreover the authority of States to overrule the national government was a belief expressed by both Jefferson and Madison in the Virginia and Kentucky Resolves which they authored in 1798. Those Resolves are a basis of the States Rights doctrine which was espoused by the Confederacy.
Yet Madison later rejected secession and nullification: "The final appeal in such cases must be to the authority of the whole, not to that of the parts separately and independently" Source.
Even Jefferson took different views of constitutional questions depending on whether he was in or out of office. Certainly, the old boy proved to be quite high-handed and authoritarian in imposing his embargo. I don't know what he would have done had a state refused to go along.
In a similar vein Jefferson Davis was never brought to trial for treason despite his repeated requests that he either be charged or released. Davis was certain that he had broken no law and it appears to be a belief shared by his captors who refused to charge him.
Hanging the b*st*rd would have set back sectional reconciliation. He was lucky that the government showed him leniency and didn't hold him to account for his actions.
Davis showed his ingratitude by inflicting his mammoth Rise and Fall of the Confederate Government on an unsuspecting country. Why that wasn't considered another hanging offense, I don't know.