You are applying 21st century logic and morality to 19th century people. That dog won't hunt. Black people, slave or free, were Southerners (usually) and expected to be loyal. You spoke about the necessity of quickly burying battlefield KIA's in mass graves, then made a vague statement implying this was somehow an exception.
It was popular for Unionists to consider all Confederates as traitors even though they were defending their homes. That is how THEY thought about loyalty.
Interesting that you ignored the comparison with the burial of dead at Camp Douglas, which was also logical. It was logical in view of people running a death camp in America.