The way you're thinking about things is very natural in the realm of computers and math, but insane in life at large.
We do not follow universal, perfect rules. Humans make judgements on what is appropriate or not based on preference.
It would be perfectly in keeping with sanity and normal behavior to decide something is worth the regrettable extinction of an intelligent species, while maintaining actual codes of morality.
It only appears that we do not follow universal, perfect rules because we have so many of them and even different from one individual to other. Our brains are too big to make sense about these rules. But if you take simple variant of brain, insect for example, you see that they pretty much have universal, perfect rules that they follow much like robots.
What's the value in extinguishing intelligent species? Otherwise you're right, but it's not in keeping with the professed morality that the vast majority of the public appears to claim to follow. As I said, it might be time to simply admit that our overriding ethic is, "Because we can."
We do not follow universal, perfect rules. Humans make judgements on what is appropriate or not based on preference.
It would be perfectly in keeping with sanity and normal behavior to decide something is worth the regrettable extinction of an intelligent species, while maintaining actual codes of morality.