If Lincoln survives with minimal or no injuries, you will see a very different Reconstruction. On the one hand, Lincoln favored a milder Reconstruction than the radical Republicans wanted, but on the other hand Johnson was much more willing to let the south get away with a lot of things that vitiated emancipation and set the stage for Jim Crow etc. Labor contracts that were basically debt peonage, groups like the Klan and White Camellia among others, the loss of voting rights all might be altered in a good way with a Lincoln directed Reconstruction. Certainly the issue of who controls the cabinet that lead to the impeachment trial of Johnson won't occur with Lincoln in office, that would be settled in favor of the president (as it was OTL) without the impeachment.
While Reconstruction won't be a paradise for the freed slaves under any circumstance, I expect things will be better if Lincoln lives as you won't have a president and a congress that are 180 degrees out from each other. Sure there are differences but not as bad as it was OTL. I think Lincoln will still be a major hero, although the halo of martyrdom won't be there.
I personally tend more to the Marfan's Syndrome, rather than multiple endocrine neoplasia as Lincoln's medical issue. Details are technical, but good odds he will live to finish out his 2nd term. 3rd term, he won't run - no crisis like depression/WWII to allow for 3rd term against tradition unlike FDR.