I imagine utterly destroying civilization in the South would have had greater consequences down the road. Besides at the end of the day, the Southern States were still American citizens.

My understanding, and I'm no historian, is reconstruction was mostly working for a couple decades after the war, until around the 1880s. Black people were able to vote, and were elected to Congress and other high offices, and won other rights, and started making a lot of progress. Then in the late 19th century the Federal government decided to stop enforcing the policies they had implemented in the South and left them to their own devices, so they started implementing literacy tests and poll taxes, and generally being oppresive douchebags, and then Jim Crow was born, and the rest is history. And most the Confederate monuments and use of the CSA battle flag, didn't even appear until the early 20th century.

Again I'm not stating this is as fact, just my understanding. Someone please correct me if I'm wrong.