I agree that there is a difference between killing enemy soldiers and killing civilians, but you'd be extremely hard pressed to find a revolutionary who didn't do both. Not every revolutionary has the means to fight a conventional war and in this case the civilians were legitimate collateral damage. Thorn didn't set out to kill civilians and (he says) he gave the confederation the means to prevent civilian deaths, but cutting off the confederation from the Lands Below is a legitimate military objective. In his other attacks (Gringotts, the schools) he has also gone out of his way to limit collateral damage. The way I see it he is waging this war as cleanly as possible while still being effective.