The Confederate army was comprised of men, many of whom died defending their homeland from what they perceived to be the aggression of an imperialistic outside force determined to impose an alien set of values on their society, obliterating their capacity for self-determination. The sad fact that these men were commonly quite racist and supported the oppression other human beings (the slaves) does not erase that, and does not mean their deaths met in war were a form of high Justice.
We have been gifted with a powerful legacy, the triumph of the Union and the cause of freedom, and it would be an abuse of that legacy to trivialize the matter. Instead, if we choose to invest the death of one of an enlisted Confederate army private with dignity and respect, one of the "baddies", we are exercising the same respect for our common humanity that impelled our forefathers to sacrifice their lives lifting the slaves out of slavery to begin with.