If we count people killed by stray bullets, all those millions of bullets fired, all those shells, and she was the only one ever hit?
I realize you may be joking, because Jennie Wade seems to be the only civilian ever talked about, and if so, then I'll add, we can count that woman who was impregnated by the minie ball at that battle of Raymond (was it?)... Seems the birth from that stray bullet cancels out the stray bullet that killed Jennie Wade--one life, one death.
More seriously, talking about deliberate shots, here's a thread just on one minor raid of the war. Have fun sorting out all those names and which were official soldiers, which were still civilians, which were militia, and therefore which counted as civilian or soldier:
http://civilwartalk.com/threads/civilians-killed-during-morgans-raid.88949/