It didn't matter if the man was a good soldier or not. I can point you to a soldier's service record from the 15th Confederate Cavalry which clearly states that he was discharged solely on racial grounds. The officers and men of his company had seen (or heard) enough evidence to show that Private Innerarity had some degree of Negro blood in him.
As far as Yankees coming South to tamper with Confederate militia rolls, let me assure you that no such thing took place. These rolls were drawn up in ink, and I have yet to see an Alabama militia roll which has any white-out on it (no pun intended). Drive up to Montgomery one day and have a look for yourself.
As far as allowing men of mixed race into Confederate service, here's a post on that very topic concerning proposed recuiting of Creoles (not slaves or FMoC).
After reading that, plus the original Confederate correspondence, are there any doubts in your mind about which way the wind was blowing in 1863?
Look at it differently. You and I might see the obvious benefit of overcoming prejudices and enrolling blacks in Confederate service. But you and I didn't live in those times. We were raised differently and reach conclusions on other reasoning. People in the past made decisions for their reasons, not ours. They didn't feel or think exactly like we do, and that's part of what makes their history interesting.