Imagine that you were a Union Army commander and hundreds of refugees turned up in a battle zone that you didn't food or shelter for or transport to take to the rear. You could try to put them up as best you could where you were. You could tell them to go away. You could send them off with an escort. None of those alternatives would be ideal. All of them would leave you liable to reproach from people 150 years later who'd never been in the position of having to deal with such a problem.
You would be operating under constraints from above. The number of rations or wagons or horses or tents you had would have been allotted to you based on the number of troops you had. Not on the number of refugees who might conceivably runaway to your lines to escape the slavers. And those generals and quartermasters above you who distributed war materiel would have to answer to Congress and the public for any resources diverted from the war effort.
Looking at various forums where this has been discussed it's striking how closely latter-day Confederate sympathizers and leftists support each other on this topic. On the Guardian site Britons who just love to attack America as racist mingle with neo-confederates who want to get back at the North. But on some of those hard-core neo-reb sites there's always one old geezer who doesn't get it and wonders why the professor is so worried about the Blacks (which was probably a more accurate reflection of attitudes at the time).
The point of _Sick From Freedom_ is that such disregard of the obvious consequences was normal - basically _no one_ in authority gave a rip for what was happening to escaped slaves.
But the slaves died in such numbers that whether genocide was intended was irrelevant. 10% of them died.