This, if possible, would be the best way of doing it.
It's not possible, no.
Minimizing civilian casualties is part of war. If you don't care, and the AI doesn't care, and you're capturing or killing civilians, that should stick with you as a penalty. The penalty is scaled by era, so it matters a lot less early on than it does in the modern period. It also bleeds off rapidly with your friends, but enemies will never forget.
It won't apply to GG/GA/Siege Towers in next version, and it'll be more painful to kill great people than it will generic civilians/diplo units. Also units in cities will be a minimal penalty.
G