And you'd be right. Just as "murder" is also a rationalization of the act of taking a life. Before laws, it was just that. Humans created the the concept of what is murder or justified. And that's why I said that the MC needs to learn or have someone teach him the difference in what his society has taught them or learn to adapt and create his own concept of taking a life. It's usually what humans do best, adapting to a situation to help suit them best so they can keep moving forward.
So, if MC is able to eventually overcome this moral issue and learn to accept that all the killing he has done has been justifiable, it may help him mentally in the future, and help get over the self loathing that comes with it.