Gerrymander the South so the Democrats can't ever win another election. Split pro-Republican chunks of existing states, and consolidate the rest to reduce representatuion i.e. combine the Carolinas, combine Alabama, Mississipi, and Georgia, etc.
Gerrymanders are double edged swords though. If all human beings were stamped with a certain identity at birth, and kept it through thick and thin, it could work, though you have to keep adjusting it for demographic shifts. Since the goal is to buy a modest amount more time for more Reconstruction to work well, you don't need it to work forever, just a decade or so might do it.
But consider that the nature of Reconstruction succeeding is precisely to change hearts and minds. It is not 100 percent just that, it is also about getting people in a disadvantageous situation into one where they are stronger and can fight for themselves (via peaceful legal means of course...but ultimately, in a knock down vigilante fight, to hold their own as well so they can't be terrorized into submission). But to an extent Reconstruction must reconcile people who OTL refused to accept freed African Americans as equals on any terms (even limited--though one reason bigots fight even limited acceptance of equality in limited spheres is that it tends to lead to broadening acceptance and eventually perhaps total social merger) to learn to live with it and even take advantage of free African Americans as useful allies. (This is exactly what the hard core of resistance to Reconstruction reviles and fears the most of course!)
Minds are in fact capable of changing. I don't think you can leverage boundaries in the South to give African Americans, all by themselves, control of everything. They have the number to control, I'm going to guess, between a fifth and a third of the South's territory, especially if they can be relocated en masse and white people moved out to compensate. But the Union never had that level of Stalinist control, any migration necessary must be pretty much voluntary.
One weakness of Reconstruction was that to an extent, it was necessary to impose dictatorial control, and in favor of the formerly disfavored Africans. To an extent a victorious Union could have justified some of that by pointing out the former slaves had in fact assisted the Union victory, they were loyal allies of Union and thus deserved some favor--an argument that obviously boomerangs against the freed people, if the local white elites regain power because then in the local setting that matters, they are the opposite of loyalists, rather traitors to an alien hostile power.
Proposing to rely on rigging political boundaries to favor one side and subvert democracy is another layer of such dictatorial control which easily is seen as oppression in itself--the only way it is not oppressive is if the side that is disfavored is accurately described as illegitimate itself. Organizing a territory so as to frustrate criminal gangs is something honest citizens can understand and support--provided the majority of citizens identify with law and order and not the "criminals!"
If instead you were to propose the formation of a separatist African American set of states--expel all white people (or those the African Americans don't approve anyway) from South Carolina, reconfigure a couple new states out of Louisiana, Mississippi and Alabama and similarly expel all unwanted whites from there, strongly urge all AA people outside these selected precincts to move while there is still time to the new black states--that might pragmatically work. It would be laden with Unfortunate Implications of course about the inability of black and white Americans to get along with each other of course, but such despair of humanistic hopes is going to seem only realistic to many people throughout the entire century and a half between 1865 and today. But logistically it is a nightmare, and politically, an outrage.
But trying to leverage control over the whole former Confederacy via gerrymandered districts? Not without rigging the elections on top of that you can't! African American majorities would be able to spread only so far, and the farther one reaches and thinner one stretches them, the more likely small demographic shifts, or difficult to suppress acts of terrorism, might flip the districts the "wrong" way and boomerang the figleaf of legitimacy. Knowing the game is rigged against them for real, anti-Reconstructionists would regard any kind of victory their side won as legitimate and sneer at cavils against underhanded or terroristic methods, calling such Cassandra cries, the kettle calling the pot black.
If one is attempting a moral reform, it is necessary to prefer the high road over the low road. Gerrymanders are generally for criminals, and the cases where they are not (majority-minority districts for instance to enable minorities to have a fair share of representation, as mandated by 1960s era court rulings and civil rights legislation) suffers by association.
Note for instance how so many reformists today say "get rid of the Gerrymander!" not seeming to realize that 1) in a first past the post election system, it is necessary sometimes to have some gerrymanders, as noted above and 2) who shall watch the watchers? I think we can get rid of the evils of gerrymanders only by finding means of bypassing district composition as determining outcomes--proportional voting in other words. Then we would not require the "good" gerrymanders either, and we could just district any old way, outrageous or straightforward, it would not matter because the true democratic majority surfaces either way. Meanwhile if we stick to FPTP, there is no such thing as politically neutral districting--someone benefits from any given scheme, and the least unfair approaches (say to devise mindless mathematical procedures to define the districts) also leave those the actions of the Civil Rights Era tried to take to protect minorities who had been systemically excluded from legislatures nullified.
So you are not wrong really in observing, or anyway disclosing whether you meant to or not, that when we have FPTP elections at all, the districts are a battleground that can empower a minority over a majority. But aside from questions of whether it is ethical to favor a minority in that way (an unusual case for it in this instance can be made after all) we have to ask how practical is it, and I think it plainly is going to boomerang hard against the people who impose it and against the people those well meaning meddlers are trying to promote.
Efforts are needed, but outrageously unfair gerrymanders are a cure worse than the disease. Don't burden the freed people with the moral onus of that on top of everything else they were blamed for! Because it is not going to win them long term victory.