Quantrill, who led the murdering in Lawrence, Kansas, was officially disavowed by the C.S.A. command. As you are probably aware, Jesse James and other later infamous outlaws served under Quantrill who used the template of war to steal and murder.
There's no evidence suggesting that when Confederate General McCausland, under orders from Jubal Early, burned down Chambersburg on July 30, 1864, that his actions were in any way not sanctioned by Confederate high command.
The truth of this matter is that we have a long list of Confederate invasions, raids and guerilla actions in Union states and territories.
Antietam/Sharpsburg & Gettysburg were only the largest of these, but there were many more, and eventually included, without exception, every Union state and territory near the Confederacy, and some quite far removed.
When Confederate forces invaded Union lands, again without exception, they took what they considered legitimate "contraband" (i.e., food, horses), and destroyed what they thought might be of value militarily (i.e., railroads).
Yes, on rare occasion they pretended to "pay for" their seizures, but only with Confederate money, which eventually became worthless.
The burning of Chambersburg, PA -- 2/3 of the city according to this source, $1.6 million in property (circa $300 million in today's values), leaving 2,000 citizens homeless, according to this source -- Chambersburg was their largest destruction of civilian property, but it strongly suggests that Confederates were as fully capable as Union forces of massive destruction, when they believed it necessary.
Therefore, the fact that Confederate destruction of Union lands was not as extensive as Union destruction of Confederate lands simply tells us that Confederates had less ability, and less opportunity to wreck havoc.
So the moral issue here is precisely the same as that of bombing civilian targets during World War Two.
Both sides did it, indeed the enemy started it, but the allied side eventually did more, and it helped them win Unconditional Surrender, and therefore now three generations of peace.
So, are we to condemn allied bombing for the lives it took, while ignoring the much larger numbers who would have died had victory been delayed by months or even years?