In Captain D. Augustus Dickert's book, "The History of Kershaw's Brigade", the southern soldiers burial were not much different that those of the men that wore the blue, or of the 54th Mass., unless a family member took charge of the body. A great deal of fuss is made of the fact that because the 54th Mass. was a Negro regiment that the southern soldiers were racist. But, according to Capt. Dickert, burials took place at the first oppertunity after the battles and southern soldier were buried the same way as Union Soldier, in shallow graves as quickly as possible. Dickert laments about the lack of concern regarding how these (southern) men were buried. And since Dickert was talking about the burial of "Southern" soldiers in this manner he can't possible have been "Racist" in his comments.
But the fact of the matter was that with so many to bury, you simply didn't waste a whole bunch of time doing it. And being "nice" about it was something that they didn't worry about too much. There are more than a few accounts of "burial trenches" for the enemy used by both sides. And even used in hospitals and camps where there was more time to take care of "Nice details" in burying the dead.
Just a few years back the "concerned citizens" of Arkansas reburied the remains of 7 southern soldiers killed at the Battle of Helena, Arkansas, July 1863, who had simply been dumped in the bottom of a shell hole and covered up. The same way the 54th Mass. soldiers were done.
So they didn't fire a 21 gun salute over them, so what.
To the soldier a dead body was just that, a dead body. And burying them was just a distasteful, but necessary normal detail to be done with as quickly as possible. I know from my own personal experience that after a while seeing dead bodies, a dead body is just another thing to deal with and nothing special to lose your lunch over. By 1864 all of those men had seen more than their share of death and dead bodies.
In the one case locally where I could say that possibly disrespect was shown to soldiers of either side, was down in Louisiana where Confederate Soldiers were seemingly intentionally buried facing NORTH, rather than the normal manner of toward the east. I have heard of cases where southern soldiers have been exhumed, such as the 7 Helena Ar. Soldiers, that were buried face down. But, one can not say that this wasn't just the way they landed when they were dumped into the grave.
Just my $.02 worth.