Freeing the slaves at the point of a gun was the right choice after the Southern traitors seceded. States' rights here are just a code for "the right of a state to decide to enslave black people".
Desegregation in the states at the point of a gun is the right choice. Keep in mind that the federal government had to call in the National Guard to desegregate schools in the South. This, to my mind, is a perfectly excellent use of force and a strong argument for government contra the libertarians and federal government contra the racists, er, states' rights crowd. States' rights or individual rights or the rights of businesses here are just code for "the right to segregate or discriminate against black people". Again, no two ways about it.
Without the Civil Rights Act, there would be worse discrimination by businesses than there is today. There is still rampant discrimination.
EDIT: For instance, an illustration from a conversation on reddit somebody had with, let me be blunt, a fool and libertarian. This is why I believe in a federal government that enforces desegregation at the point of a gun. Because it won't happen otherwise and segregation is a worse evil than parading around with a gun (don't these people like the idea of parading around with a gun, anyway?).
ANOTHER EDIT: the reasoning in that link reminds me of the recent Supreme Court ruling on the Voting Rights Act. And after their ruling, the states went on to enact a series of measures whose obvious intent was to curtail minority voting. If anybody needs me, I'll be in the Angry Dome.