I really don't see your Article 1 argument. Article 1, Section 8, (8.1) addresses "common defence", while Section 9 (9.2) addresses suspension of Habeus Corpus during rebellion or invasion (for public safety). The southern States withdrew from the Union, they did not rebel, they did NOT invade the northern States either. The secession was debated loudly within each State and not lightly either.
The Whiskey Rebellion and Shay's Rebellion's are not applicable, both were contained within a State (PA & MA respectively, note YANKEE), both were economic in nature (taxes for one, and sour economic conditions for the other). The Shay's rebellion took place prior to our Constituion's writing and acceptance.