The situation you're describing is akin to two tribes living in a territory with enough fresh water for only one of them.
The options are clear. Either one tribe dies or the other one dies.
The other side will die together with all of its civilians regardless of whether you'll target them or not as long as you do not die, because this would mean they have no fresh water, so it seems pointless to avoid it.
I would however avoid targeting civilians since the side that lives on needs to live with its actions after all is done and settled, and I see no advantage at all to be gained from targeting the civilian population of the other side. The war will be settled by the last soldier standing not by the last innocent baby or innocent old man standing.