No punishment is needed, after a war of that size, there is no need to damage a new set of states in America. That would just set us back even more in the steps of reconstruction.
CSA soldiers and politicians would treated as normal citizens, since we are making them into the union, we shouldn't start to treat them different as that would cause them to push back.
The new freed African Americans would have a hard time fitting into society at first, as it would be a massive change. A way to troubleshoot that would be for them to be educated on some common manners and public behavior that way they can be ready for society.
Industrializing the south
Not only would this provide entry level jobs for freed slaves, but it would boost the economy and help repair the south. With cheap and fast production, the south would be back on their feet in no time and the slaves would have many job opportunities.
Of course people will be against this at first, but like always, it's hard for people to accept change. If the freed slaves were educated on proper manners and the way they carry themselves, racist white people would see them differently, and as humans, not lower beings.