I certainly by no means meant to underestimate the damage down to the South during Reconstruction. After Reconstruction The South began to slowly recover, but the political freedom which the former slaves had enjoyed in the ten or so years after the Civil War also began to disappear.
With the Union army gone, organizations like the KKK and several others, which traced their roots back to the Reconstruction period , regularly used violence and intimidation to reduce the number of black voters to a trickle. In the South segregation was given enshrined in state and local laws and while blacks were certainly kept separate they were by no means treated equally. Poll taxes, literacy tests and other discriminatory practices were incorporated into voting laws to hold down the black vote ensuring the status quo.
That sad state of affairs continued for nearly a hundred years until things began to change with the advent of the civil rights laws in the mid 1960's. We have come a long way in the last 50 years, but the events in Charleston remind us that we have some distance to go before we can remove the hate which still burns in the hearts of some people.