Other than trials for confirmed war criminals, I think it would have been both a short-term and long term mistake to arrest and execute Confederate civilian and military leadership as traitors (although they obviously were) or engage in draconian and unconstitutional land redistribution practices aimed at eliminating the planter aristocracy. The OTL leniency has set a precedent for the US to be relatively lenient in dealing with other defeated enemies, convicted political subversives, deserters, draft-dodgers, individual traitors, and others in the following century. Had the US government executed several hundred or a thousand Confederate leaders after the Civil War as traitors and forcefully expropriate legally owned land from thousands of private citizens for redistribution to freed slaves and others, all sorts of awful precedents would be set. In fact, I question whether the traditions of American democracy would survive.
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