Black slavery was the heart of the struggle between the states. As the history of “Bleeding Kansas” attests, the issue could not be resolved through the ballot. The South demanded that its “system” be allowed everywhere in the Union. To avoid session in 1850, the North —and at this time this included the Border states—agreed to split the difference, granting the southern half of the Mexican Cession to be slave territory, along with Texas but excepting Southern California. They also passed the Fugitive Law Act, which was as blatant a violation of States Rights as one can imagine, because its violated the principle that the State was the basic political unit of the Union. Under the Constitution, the State was the primary protector of the rights of its inhabitants. So the South was willing to violate the sovereignty of the northern states in the interest of its “Peculiar Institution.”
But Kansas was resolved through the ballot. Arguing it presaged the war holds about as much water as saying John Brown revealed the North’s secret plans.
You bring up the Missouri Compromise, but for some strange reason fail to mention that it worked and along with Dred Scott it practically settled the issue of the westward expansion or nonexpansion of slavery. Despite countless history books, that was not at issue. Slavery had nowhere to go, at least not in that direction.
As for the Fugitive Slave Act, it did override state prerogatives, but it was not destructive of state rights or the federal system as you imply. The federal government had various powers wand no one of them makes the states slaves to it. Especially not federal powers that people generally assent to, and despite abolitionists the fugitive slave law was not unpopular. Republicans in fact proposed strengthening it through constitutional ammendment.