All of them should've been tried for treason. The main political leaders should've been executed. I'm not so sure about some of the military leaders, particularly Robert E. Lee, who at least was not convinced of the morality of slavery.
I think the largest plantations should've been broken up and land given to poor whites and blacks. Federal troops should've stayed in the South at least until the end of the 19th century to ensure blacks got all the civil rights they deserved, particularly the right to vote.
No matter what the neo-Confederates say, the Civil War was fought fundamentally over slavery. All of the leaders of this breakaway nation were fighting for this inhumane institution and should have faced justice. Many deserved execution. The disaster that happened when Hayes ended the Reconstruction shows that federal troops needed to be mantained for as long as was necessary to protect blacks.
Just to prove to you that the civl war wasn't fought about slavery, let us explore two alternate realities:
1) The CSA wins the war. Due to their free trade policies, other nations such as Britain use it to encourage them to abandon slavery. Reluctantly, they do, as it would be uneconomical for them to do otherwise, and prosper from their trade. Without the disastreous perios of Reconstruction, Southerners don't blame their problems on the free blacks, thus preventing the world from having to feel the wrath of the Ku Klux Klan. Ultimately, the South promises to reneter the Union if they have lower tariffs. Under threat of seccesion, Woodrow Wilson is unable to become presidenet, thus saving the USA from the Federal Reserve, the income tax, and WWI.
2) The USA wins the war before the Emancipation Proclamation. As Licoln promises, the 13th Amendment (which would have made slavery legal) is passed. Due to Lincoln's protectionism, other countries cannot manipulate the USA into abandoning slavery. The horrible practice of slavery takes several more decades before it can be abandoned.
