The point is that if a state SECEDES, then it is no longer a state, but a nation, and therefore, no longer bound by the Constitution. Therefore none of the prohibitions would apply.
free dixie,sw
Was South Carolina a state in 1860? If so, the Constitution did not allow them to form a Confederation, raise an army, etc. There was no secession clause in the Constitution negating the prohibitions.
I think that the perpetual union spoken of in the Articles of Confederation is also pertinent. If the earlier document was meant to be perpetual, the succeeding document where the people wished to make the union more perfect was also meant to be perpetual.
The states never had an autonomous sovereignty apart from the United States. They started as colonies of England and only became separated from this dependency under the United States in the body of the Continental Congress. The Union not only predated the Constitution but also predated the transformation of colonies into states.