Does the Torah Recognize the Existence of "Innocent Civilians"?

Modern-day nations – Israel chief among them – avoid harming "innocent civilians."  But do such people exist?  If they did, why did G-d punish the Egyptians as a collective?  After all, the plagues affected every Egyptian, not just the guilty.  Indeed, the Plague of the Firstborn even affected foreign captives in Egyptian jails according to the Midrash!