Reconstruction did funny stuff and the mindsets at the time were different. The entire idea of the civil war centered around if we had a federal or confederated government. The confederate argument was states had to ratify the constitution, so therefore they could deratify and break away. Looking back this is obviously wrong, but a large minority of people believed this at the time, including the 15th President I believe. On the other hand, since Lee surrendered unconditionally, the thought process was you don’t kick the man while he’s down. Plus many men in the Union still considered Lee a heroic American figure. Not imprisoning him most likely led to an easier surrender by the rest of the Confederate forces and less paramilitary actions. Reconstruction further limited the punishment of top officials which was a mistake, though there was 0 chance they could end the thoughts and ideals that led to jim crow and the kkk, they could have certainly limited it.

Remember that Benedict Arnold is famous for that. Not saying anyone beats Lee, just that this happens from time to time.