I do think the morality system is designed with the assumption that the characters will make choices that cause conflict, and a group that does not do that will jump to 100 pretty quickly.
In the specific example of killing a helpless bad guy, the rules call for 10+ points of conflict. If your group believes that a character who kills a helpless enemy should lose a lot of morality, then assign a lot of conflict for such an act. The rules suggest a minimum of 10. There is no reason you could not go higher.
That said, if you don't enjoy the system, and prefer something else, then that is what you should do and no one should be offended by it.