I think that the enormous difference in population size between the Mormons and the Confederates makes that a logistical impossibility. The regions the Germans were expelled from were not the most highly populated parts of the country, and the US could use those resources far more efficiently to simply occupy the south instead of spending them on a costly ethnic cleansing campaign that strips them of the moral high ground both at home and abroad.My personal theory is that the US would essentially ethnically cleanse most of the Confederacy of it's white confederate populace. Completely or almost completely expel the non loyal populaces to one or two of the pre war CSA states that are seen as less valuable. Say Florida or South Carolina. Force the rest of the Confederate populace to move their at bayonet point. A lot of people would die but it'd be less "Holocaust" style genocide and more the mass expelling of Ethnic Germans from across Eastern Europe post WW2. The remaining Confederate "Reservations" wouldn't be really independent any time soon and would have any and all industry demolished or confiscated and dismantled. No real formal CSA armed forces would be allowed to exist and pretty much all the weaponry the US authorities could get their hands on would be confiscated. There'd be plenty of US garrisons to police the Confederates. It'd be awful in a lot of ways but I think it's the route they'd go over trying to police the entire former Confederacy. Easier to just have to police and control a state or two. After expelling the White Confederate populace from much of the former CSA you'd likely have the land divided up into modern "Land Grants" like was done OTL in the West in the late 1800's. Offer a certain amount of land to any American willing to settle and farm. Nationalize or sell off the remaining industrial assets/mines/the like.
Their was talk late in the last book about essentially doing that to the rebellious Mormons. Namely expelling them to one of the less valuable Hawaiin islands. I could see the US similarly expelling Mormons to Alaska. Quite possibly they'd also expel any "disloyal" Canadians to Alaska, Nunavut, and the like. Perhaps expelling some of them over the border into Mexico or paying some country to accept Canadian, Confederate, Mormon refugees.