While the Civil War denied de facto and the SCOTUS subsequently denied de jure (or ex post facto) the states' right to secede, it was firmly established during the Constitutions ratification process. Again, without explicit assurances to the several states that they DID retain the right to withdraw at will, that ratification would probably never have occurred. That coupled with the powerful arguments the Constitutions author made for secessions legitimacy make it hard to see how secession is on the same level as Marbury v. Madison. There is a great difference between a federal power spontaneously claimed as a given and a state right affirmed by the Constitutions author and vital to its ratification.

As to the Civil War specifically, again, though slavery was inextricably bound up with its larger and longer enduring issues, it was far from the whole or even primary reason. Many Northern leaders were far from champions of slaves just as many Southern ones were far from champions of slavery (though, if memory serves, Davis WAS an advocate of slavery, as such.) For one thing, the issue of secession itself loomed large for the reasons already discussed, and had done so for decades during which most Northerners were no more averse to slavery than most Southerners. Secession first reared its head in practical terms when NORTHERNERS came to resent and even fear Virginias status as "The Mother of Presidents," not because the good people of MA felt their "right" to own people was threatened.

Fundamentally, the Civil War was more about the balance of Northern vs. Southern and mercantile/industrial vs. agrarian power than slavery. Likewise, popular sovereignty was more about those issues than about slavery; it was the only viable alternative to the Wilmot Proviso or an equivalent permanently confining planters to the existing Southern states while Northern industrial and mercantile interests spread across the continent until they dominated the political system. That was the real crux of the Civil War: Whether America would be, and be ruled by, yeoman farmers self sufficiently living off land they owned and thus independent in fact as well as name (as Jefferson envisioned,) or a mercantile industrial nation. Needless to say, the latter view prevailed by force of arms rather than law, and all Americans, regardless of color, were "freed" to owe their soul to the company store. Former slaves in the South enjoyed a brief period of political power before their liberators celebrated the centennial of America freedom by betraying them with the Corrupt Bargain of 1876, looking the other way as the South inaugurated a century of Jim Crow in exchange for the presidency. All uncertainty about the Civil Wars root cause vanished then; the Civil War was, on many levels, the culmination of the conflict between Jefferson and Hamiltons vision of America, finally and bloodily decided in the latters favor, with slavery a largely incidental concern. A century and a half later many of the same rural vs. urban and agricultural vs. industrial conflicts remain bitterly divisive, because they were never really addressed.

The tragic irony is that not only should the Civil War not have been taken as a(n unconstitutional) revocation of states rights, but that ending slavery was itself eminently constitutional under the very Amendment the Civil War is invoked to dismiss.
That statement contains a very clear order of precedence that should be obvious to anyone familiar with Constitutional law. Powers the Constitution does not grant the federal government or deny the states resides with them. Yet what of powers not granted to the federal government that ARE denied to the states? "Or to the people" covers those powers by exclusion. If there were any ambiguity, the Ninth Amendment ought to remove it: That means that just because the Constitution does not explicitly state one person may not own another does not deny anyones freedom not to be owned. Article IV, Section 1 of the Constitution states, while the 1st Clause of Section 2 further states, and if even THAT is too vague, Wikipedia quotes the SCOTUS in Corfield v. Coryell (in 1823) stating that includes That does no invalidate the Fugitive Slave Clause, per se, but DOES make it effectively useless for pursuing fugitive slaves rather than other people

More simply, slavery is not a valid application of states rights, but an invalid and unconstitutional infringement of the peoples rights under the Constitution. Acknowledging and correcting that injustice was not only possible but obligatory. Failing to clearly and firmly establish that principle was bad enough, but doing so in preference for unconstitutionally dismissing states rights (which continue to be selectively invoked and repudiated as convenient) was unconscionable. Not only did it attach the stigma of racism to the Constitutions vital defence of states rights against federal abuses, but the principle that no man has the "right" to abuse another continues to rely on the several states to establish it to whatever extent they wish (or not.) Ironically, the denial of THAT right in cases like gay marriage and abortion is one of the areas where many still value states rights. That, of course, only underscores the need to draw the distinction properly, however belatedly; no state has the right to order anyones personal life, not because state rights are invalid, but because personal rights must trump state authority as assuredly as states rights must trump federal authority. In both cases, the superior authority is predicated on and exists to serve the rights of its constituents.