"My mother and I went to Shiloh a long time ago, and I will never forget her looking
at the burial pits saying, "Just look how they treated our boys."
My message was that these men were better than the the way they were treated
whether they got the burial pit or the swamps, it was a terrible disgrace in my
opinion."

I wonder:

Who was left behind to identify these dead men? What other option was there? Leave their bodies to rot in the air, carried away by wild animals, to feed local hogs? That certainly would have been a deep insulting disgrace. A common burial pit resting with their companions was never intended as a disgrace, it was a mercy, and a matter of great urgency as the bodies quickly decomposed, and so it was about the best that could be done under the circumstances. With the Union dead there was at least some chance of identification, therefore some effort was made to do so, and they were then buried as individuals. Individual identification of the southern men was simply impossible.

When victorious rebel forces held the field in battles like at Pleasant Hill the situation was reversed of course, and Union dead, with no one available to name them, were buried unidentified, often in one large grave. The secessionists were more apt to be identified by their friends, it may not always be possible, but the chance was there, and because of this effort were buried with individual honors by their comrades.

Only after the War was over were such group graves of Union men exhumed and the jumbled unidentified remains symbolically separated and given 'single' burials in National cemeteries as Unknowns.

Unlike the dead at Fort Wagner, where it was an announced policy specifically meant as deliberate insult, to toss human beings into pits with no more dignity than dead cattle, these southern men at Shiloh were given a burial as respectful as conditions allowed. No modern person need read insult into the mass graves at Shiloh. Shiloh was not Treblincka.