Are you saying Madison's opinion of the Constitution was no longer "operable" in 1861? Does that mean you agree with the "living Constitution" advocates who say the Constitution's meaning changes over time?
And I agree the Founders spoke quite clearly about the right to Revolution. And you confuse the right to revolution from oppression with a fictitious right to secession without cause. Madison addressed you confusion very directly in 1833.
"I return my thanks for the copy of your late very powerful Speech in the Senate of the United S. It crushes "nullification" and must hasten the abandonment of "Secession." But this dodges the blow by confounding the claim to secede at will, with the right of seceding from intolerable oppression. The former answers itself, being a violation, without cause, of a faith solemnly pledged. The latter is another name only for revolution, about which there is no theoretic controversy.
The Civil War was a Revolution without cause -- unjustified since there was no "intolerable oppression" occurring. The Federal Government had every right to put it down. There were not being oppressed in any way. There was no right in the Constitution then, and there is no right today, to unilateral secession.