It is something I have given a great of thought to in my own TL. Political office holders under the CSA Government has got to be on that list. General rank in the military I think as well. State governments are tricky (particularly those that did as much harm as good to the CSA by their states rights stances!). Non-commissioned men cannot be on the list especially not where there was conscription. I did consider slaveholders but as has been pointed out it was perfectly legal at the outset of the war. Company and regimental officers I am ambivalent about.
I view this as one of the worst problems - the US government left the old elites and power structures in place. The reconstructionist state governments had neither breath or depth of support. A massive sea change was needed to 'remove' the existing political elites and redistribute power so that a larger and broader (i.e. more than just freed slaves) would support the reconstructionist state governments. Confiscation and redistribution of land might assist in achieving that in the short term.
I agree also that a competing narrative needs to be created to fight/overwhelm the "Lost Cause". Trials for treason (if convictions could have been secured) would aid in this. I know that legal opinion baulked at the likelihood of convicting Davis but there were army officers who blatantly broke their oaths. If there was truth in the 'slave raiding' during the Gettysburg campaign or 'war crimes' like the execution of African American prisoners or the treatment of all Union prisoners of war then these should have been prosecuted. I cannot believe only Wirz can be made into a 'bad guy'. I have seen the photos of Union prisoners and I initially mistook them for WWII Holocaust survivors. A decent PR man could have made mincemeat of the Confederate reputation during and after the war but the narrative seemed to be left the former Confederates themselves to set.
Yeah, you'd need both a) some kind of trial/hearing/commission that would dismantle and "deal with" (either through imprisonment, execution, or stripping of citizenship) the senior members of the Confederacy, and b) totally uproot the Planter political class and remake the social order (basically, turning the poor whites against the elites), while at the same conjuring a narrative of the Confederacy as a self-inflicted wound, one that the Union was ready to cure.
It would be a serious undertaking, we'd be talking land reform, troops deployed for a least a decade, one of the largest and most in-depth PR campaigns that had ever (or probably would ever) be waged. You'd need a real, top down commitment from the US government to see the reshaping of the South through, but my guess is that if you could get the poor white veterans of the war, and the subsequent post-war generation to "buy in", you'd have most of the work done for you.