I don't think Old Whig planters were really enough to control the South either. Again, if the U.S was framing policy in terms of forming a majority coalition, non-slaveholding whites are where you want to focus on, in addition to draftees and deserters, those with the weakest attachment to the Confederate cause.
Ex Whigs turned out an impressive vote for John Bell in 1860, and a respectable one against immediate secession in the ballots for State conventions. Combined with Unionists from the mountain regions (who had mostly been Democrats before the war) they are probably in with a chance in at least some parts of the South.
I don't see why previous attachement to the Confederate cause should be that much of an issue. It would matter if the ex-Rebs were permanently estranged from the Union, and looking to a second rebellion but the vast majority weren't. Frex, Longstreet had been as loyal to the Confederacy as anyone, yet became a Republican in the Reconstructiion Era.
In any case, though, Lincoln doesn't need the Republicans to rule all the South - just a few states will do. The GOP already has most of the North, so the only way they can lose is if the Democrats carry all the South and Border States, plus NY. So 20 or 30 reliable electral votes from below the Mason Dixon line ensures Republican copntrol of the national government.
Hence a Federal Homestead Act for the South, and possibly the extension of government loans. The main thing is a tangible demonstration of the national government's identification with the smallholder, so as to stimulate cross-racial class politics.
There was a Southern Homestead Act, but it had little effect.
What "loans" are you suggesting should be extended? Keep in mind the country is paying for a huge war, so anything that requires major spending is ASB.