Morality is defined as I stated, a code of conduct, the set of standards that dictates what is right and wrong. For the purposes of this discussion, however, I believe morality can have more than one definition, and yours fits as well. But that’s beside the point. The larger moral problem is the immense cost of war—on human lives, on economies, on resources, etc.—and so it’s really not about tolerating, as you say, atrocities in exchange for peace.