Maybe you could have black militia's armed with surplus Civil War Rifles, like in the TL We Will Have Peace.
There were Black militias OTL. I presume that they had rifles, though offhand I don't know the source. But it didn't really matter. With a million or so Confederate veterans in the South, the other side had virtually unlimited manpower to call upon.
Getting back to Mr Lincoln, I suspect he'd have gone for something along the lines of Senator William Stewart's 1866 proposal. Stewart (a Nevada Republican) wanted something along the lines of Horace Greeley's "universal amnesty and impartial suffrage". Franchise laws must be colour blind, with any literacy or other tests applying equally to blacks and whites alike. This pill would be sugared by a total and unconditional amnesty, so that all treason trials, confiscations or disfranchisements would be wiped off the agenda. Iirc, Alexander H Stephens and other prominent Southerners were favourable to the idea, but it got swept away in the grudge match between Congress and Andrew Johnson. Since Lincoln would almost certainly not get into such a fight, I could see something like this going through.