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.
"It depends on the state itself to retain or abolish the principle of representation, because it depends on itself whether it will continue a member of the Union. To deny this right would be inconsistent with the principle on which all our political systems are founded, which is, that the people have in all cases, a right to determine how they will be governed."
And while there is no hard record of what particular texts were taught at West Point, Charles Francis Adams wrote that Rawle's view was taught at West Point right up to 1840.
Charles Francis Adams' view on the subject is well worth considering. Adams was about as Yankee as you can get, the great grandson of John Adams and a Union General to boot. He made a speech in 1902 'The Constitutional Ethics of Secession' where he examines the very subject we debate:
"When the Federal Constitution was framed and adopted, an indissoluble Union of indestructible States, what was the law of treason; to what or to whom, in case of final issue, did the average citizen owe allegiance? Was it to the Union or to his State? As a practical question, seeing things as they then were, sweeping aside all incontrovertible legal arguments and metaphysical disquisitions, I do not think the answer admits of doubt. If put in 1788, or indeed at any time anterior to 1825, the immediate reply of nine men out of ten in the Northern States, and of ninety-nine out of a hundred in the Southern States, would have been that, as between the Union and the State, ultimate allegiance was due to the State."
The whole speech can be found here:
"Later" is the operative word in your statement.
When the States acceded to the Constitution there was an understanding, which Madison spells out in the Federalist papers. Madison was also in agreement with the State of Virgina's understanding of what was delegated and what was reserved. All these understandings were brought to the forefront in the Report of 1799 when he said:
It appears to your committee to be a plain principle, founded in common sense, illustrated by common practice, and essential to the nature of compacts, that, where resort can be had to no tribunal, superior to the authority of the parties, the parties themselves must be the rightful judges in the last resort, whether the bargain made has been pursued or violated. The Constitution of the United States was formed by the sanction of the states, given by each in its sovereign capacity. It adds to the stability and dignity, as well as to the authority of the Constitution, that it rests on this legitimate and solid foundation. The states, then, being the parties to the constitutional compact, and in their sovereign capacity, it follows of necessity, that there can be no tribunal above their authority, to decide in the last resort, whether the compact made by them be violated; and, consequently, that, as the. parties to it, they must themselves decide, in the last resort, such questions as may be of sufficient magnitude to require their interposition.
Madison's Virginia report is very consistent with what he said this during Virgina's ratification:
That resolution declares that the powers granted by the proposed Constitution are the gift of the people, and may be resumed by them when perverted to their oppression, and every power not granted thereby remains with the people, and at their will. It adds, likewise, that no right, of any denomination, can be cancelled, abridged, restrained, or modified, by the general government, or any of its officers, except in those instances in which power is given by the Constitution for these purposes. There cannot be a more positive and unequivocal declaration of the principle of the adoption that every thing not granted is reserved. This is obviously and self-evidently the case, without the declaration.