I posted below some general thoughts about the limits of "institution X brought bad result Y, so X is bad" reasoning. Let me mention a few more general things about the claim that federalism / states' rights is tainted by its use as a means of advancing segregation.
The terms "federalism" (at least in its the sense it's used in political debates) and "states' rights" are generally relative terms, not absolute ones. When someone says he's in favor of "states' rights" or "federalism," that usually means that he supports more state authority about the topic at hand than his rivals do, or than the status quo provides. It almost never means absolute, unlimited rights for states, whether in general or even in a particular area. For instance, even those who speak of traditional areas of state supremacy, such as family law or education, very rarely oppose some degree of federal regulation, for instance the federal tax code's treatment of marital relations (which surely has vast indirect effects on state-recognized marriage) or the parental rights decisions that bar states from mandating that all children go to public schools.
This is surely true in current debates about the U.S. Constitution. The debate on the Court isn't whether — as a constitutional matter — we'd have 100% federal authority with no limits vis-a-vis the states (but only with limits created by intra-federal separation of powers principles, or by individual rights against federal authority) or 0% federal authority. It's whether we'd have 99.9% federal authority (perhaps with a very few highly uncontroversial examples, such as the federal government's being barred from creating states within an existing state's boundaries without the state's consent) or 95%. Justice Thomas, the one Justice on the Court who takes the broadest view of states' rights, might go for 90% or maybe 80% federal authority. [WARNING: Numbers used figuratively, not as concrete estimates.]
Likewise, the debate in Congress or in other mainstream institutions isn't whether — as a policy matter — we'd have 100% federal authority with no authority for the states, or 0% federal authority. It's whether we'd have, say, 70% federal authority or 30%. Everyone agrees that some things are best done at the state level, though often with some federal input. Everyone agrees that other things are best done at the federal level, though often with some state input.
Let's focus now specifically on segregation: The original Constitution clearly left states with a great deal of authority over how to govern conduct within their boundaries. On the other hand, the Fourteenth Amendment clearly constrained that authority in some significant measure. Likewise, the original Constitution clearly left states with a great deal of authority over who could vote, but the Fifteenth Amendment clearly limited their legal power to discriminate based on race; segregation persisted in many places largely because the Fifteenth Amendment wasn't complied with. One could support state autonomy in many ways but conclude (as a Congressman or as a Justice) that segregation and the right to vote without regard to race is an area where the federal government (acting both through the Court and through Congress) should have broad authority. Conversely, one could support federal power in many ways but conclude that for various practical reasons the federal government ought to have left this matter to the states. (That's not my view, but it's a view that some could and did take.)
So it's not clear that the civil rights era experience even tells us that much about the value of federalism and states' rights. It might illustrate that some calls for state authority rather than federal authority might sometimes support immoral and unconstitutional programs. (There's debate about whether separate-but-equal segregation should have been understood as unconstitutional under an original meaning approach to constitutional interpretation, but separate-but-unequal segregation — which is what segregation usually was — surely was unconstitutional, as was the massive racially discriminatory denial of the right to vote was unconstitutional.) But that just means that the segregationists' proposed state-federal balance as to race discrimination and voting was improper. It tells us very little about others' proposed state-federal balances as to other topics.
In this respect, federalism is rather like individual freedom from government restraint, or government power, or many other concepts. That a particular proposed individual freedom from government restraint (e.g., freedom from government restraint of parents' abusing their children) is improper doesn't by itself tell us much about the propriety or not of other freedoms, or even other parental rights. Likewise, that a particular proposal for state freedom from federal government restraint is improper doesn't by itself tell us much about the propriety or not of other proposals for state autonomy.