Roughly 1/3 casualties in war are soldiers and the rest are civilian. Such is the world I'm afraid and its not like you're not able to kill innocents and civilians in other games as well, shooting doctors in the head so the skull fragments fly all over in Half-Life, random beat downs in GTA as mentioned and countless other games feature this possibility.
I haven't really seen a game with a level where the objective is to actually kill innocents though.
PS: I was truly shocked to learn that the evildoers were Russian, very original...









