Actually, Albert Pike (Arkansas, I believe) commanded several regiments of Amerindian troops.
There were also, several regiments of free Black troops serving in the Confederate Army, from New Orleans I think.
One of Grant's officers, who was with him at the surrender at Appomattox and drafted the surrender document, Ely S. Parker, was also an Amerindian.
Yes, thousands of blacks did serve willingly in the CS army. Many good books have been written on the subject. I also know quite a few descendents of black soldiers and they have no shame for what their gggrandfathers did.