The Slaughter House cases effectively rendered the privileges and immunities clause of the 14th Amendment, which had been intended to guarantee individual rights vis-a-vis state governments, a dead letter.
Eventually, courts figured out how to work around this problem by selectively incorporating important parts of the Bill of Rights into the due process clause of the 14th Amendment which is also effective against state and local actors. But, this took time and remains an awkward theory to buttress federal protections for civil liberties. Some rights took half a century, and others nearly a century to secured federal protection in the wake of the Slaughter House cases.
But, the cleaner approach, by far, would have been to rule only narrowly in the Slaughter House cases themselves, which did not require such a broad ruling to be resolved, and to use the privileges and immunities clause of the fourteenth amendment as the legal basis for federal protection of the civil liberties set forth in the bill of rights.
The episode taken as a whole is vibrant proof of the legal realist view that the values of the people implementing the law greatly impact how the law is applied in fact.