Confederate resistance and punishment?

They were traitors because they lost. Many fought because they felt their homes had been invaded by the North, others for the principle of State's Rights(yes, including slavery), and others simply because of simmering resentment of the North. But the point of Reconstruction was to convince these men that they were indeed part of the United States. Some political leaders were imprisoned for a time, and all were stripped of their Citizenship. However, the majority of Rebels were allowed to regain that citizenship upon taking an oath to the US, as well as meeting a few other conditions. There was no organized resistance once the news of Lee's surrender reached the further areas of the Confederacy. Generally the North did not impose any harsh punishments on the South, though "carpetbaggers" were notorius for abusing their powers for personal gain when coming South to oversee Reconstruction. The most contentious part of Reconstruction were the new rights granted to the freed blacks. The Republican party was the staunchiest in seeing that those rights were backed by the political and military will of the US, but by 1776 the Republicans would "sell out" and agree to withdrawal of US troops in exchange for Democratic agreement not to contest the electoral outcome of the Presidential election that year.