AS a person, Lee had many fine qualities. As a public person, not so much. He saw his first loyalty to the state of Virginia, NOT the United States, which is why he was on the fence until Virginia seceded and then resigned. While he may have personally seen slavery as an evil, he was not so ignorant as to fail to understand that the "right" that created the CSA was slavery - there were other issues but slavery and its preservation (and extension) was the overriding issue. In terms of constitutional interpretation, the Constitution replaced the Articles of Confederation, precisely to give primacy to the federal government, leaving to the states those powers not given to the federal government. Secession was not mentioned at all, the rationale behind secession was "we decided to join so we can decide to leave". Whatever that was it wasn't a "constitutional" argument.
Reconstruction could have been much worse. Treason trials for senior CSA government officials and general officers. Lifetime disenfranchisement for any CSA government official (state or national) above a certain level - the local mayor or postmaster gets off, state legislators, high bureau officials disenfranchised. Likewise officers in the CS military disenfranchised, enlisted not. Confiscations of land and money of slave owners for redistribution or paying for things like housing and schools for Freedmen. Making state constitutions protecting the franchise for Freedmen, and preventing segregation a requirement for readmission. Most of these were suggested at one time or another, and could have been easily imposed. While they might have increased white resentment (although not sure how much that would have been possible) some of these could have been beneficial. BY putting penalties political and financial on the planter class and their allies, who were the driving force behind secession, much of their power is gone - yet none of these penalties directly hurt the yeoman farmer, physician, or artisan in the white south. The reality was that most of those who were political/social elite/wealthy before the ACW regained or retained those positions in the post war period. By removing their political influence, and their ability to influence things through money will allow the possibility of a better reconstruction.
It is worth noting that only about 25% of southern households owned slaves, and most of the slave owners owned few. While emancipation represented a significant financial loss to slave owners, as well as disruption of their labor force (later recovered through labor contracts and sharecropping), the 75% of southern households who did not own slaves suffered no direct loss due to emancipation. It is worth noting that many in the CS political upper class bruited about the possibility of reinstating property requirements for the franchise which would disenfranchise many whites - but this would be OK because they would still be above blacks on the ladder permanently. The scenario posited here could allow for some commonality of interest between freedmen and non-elite whites in the south to develop. Not kumbaya making s'mores, but better than OTL.