Reconstruction and its aftermath created some serious battle lines. Sadly, at that time there was no way a group of white Southerner ex-Confederates was going to "officially", on paper, give any credence to black assistance of any kind during the war. Not after carpetbaggers and scalawags had used black democratic votes (and vote fraud on a massive scale) to vote themselves money and power, while disenfranchising the Confederate veterans.
That's why contemporary documents are of greater value than the backward glances of the Old Boys after the colors fade.
But, as usual, the official rhetoric was belied by the actual conduct of folks on the ground in their relations with people that they knew. In addition to the story of gg grandfather's former slave, some of my cousins' family were Confederate Veterans over in Rome, GA, and I know from reading a history of the city that there was at least one black member of their organization. He raised fighting chickens, I think, and he frequently brought his prize roosters to the reunions. (That oughta get the PETA maniacs riled up, huh?)
Well read the article mom. The author clearly stated that the CSA could have saved itself if in 1862 or 63 it had allowed freedom for service. By eliminating 35% of its adult male population from active service while gradually watching that same population move into service for the enemy, the CSA doomed it's chances. The author is lamenting the fact that blacks couldn't serve the CSA. He wished they could have.
As to you saying that “reconstruction” poisoned race relations, I would suggest that the Black Codes enacted by Southern legislatures that attempted to circumvent the 13th Amendment and re-establish slavery poisoned relations and lead directly to reconstruction. When reconstruction ended, those same legislatures wasted no time enacting new codes in the form of Jim Crow laws. The southern power structure simply refused to allow even the hint of equality under the law.