I think the Civil War's outcome killed the notion of the federal government being subordinate to the states.
No. The fighting of the war to begin with did that. The South, in their zest and zeal for self destruction, went down a path of infinite regression whereby, day 1, it was, at best, a duplicate of the union they just left and, by virtue of going to war, a war most of the major league deep South big mouths thought they were physically immune from due to the unthinkability of any actual Northern invasion coupled to shear physical distance in a nation most young men had never been more than a days horseback ride from their homes, set in motion centralized forces that, at the same time, were excessively sensitive of state sensibilities while embarking on a venture that demanded central authority.
The South had everything in their favor to continue in the Union, to deal with the death of slavery, over time and pretty much on their time schedule, peacefully. And then there was Southern Pride that said we'd rather lose it all than...than what? Accept a abolitionist President who thought, and said, "If I could end slavery I would not. If I wanted to, I could not." Further, if Lincoln issued the Emancipation Proclamation on day 1, he'd have had no army.
Furthermore and lastly, the ONLY thing Lincoln was fighting for was to save the Union. He'd have done ANYTHING, including left things be, to avoid the split.
Southern pride killed this nation and changed it from These United States to THE United States. All the forces of centralized power Madison so adored were unleashed in the fury, passion and emotion of civil war.