Well, Firaxis is making game where you can conquer people, soldier killing each other and nuking imaginary million innocent civilian. Why? Because IT'S WAR. We can't say that the history of the Earth have no war. There are actually lot of it.
Being victorious or defeat in war is what the real history have. "Nice people" often get conquered by "Strong people". Civilization (the game) is not SimCity, and according to Sid Meier's interview in CivBE. He wouldn't make peaceful game just because the war is actually horribly bad. He want to make game and make player thinks like, "What can I do".