I think I understand your basic mistake. You seem to think that morality is objective in a way which is unrelated to the particular kinds of beings that have that morality. So for example you might think that killing innocent persons is wrong regardless of the particular history of those persons and their species.
This is a mistake. For example, if people had evolved in such a way that reproduction required the killing of one of the persons, but it consistently resulted in the birth of twins, then killing a person in this context would not be wrong. This is not because morality is or would be subjective, but because it would be objectively right for that species existing in that context.
In the same way, people have evolved as meat eaters. They consequently evolved to assign extremely low value to the lives of other edible creatures, and this is objectively correct for the human species, even if it might not be correct for some other kind of being.
Nope, I still think that's wrong. It can't be helped until they develop better technology maybe, but it's wrong. The species in Greg Egan's Orthogonal series was like that. They eventually figured out how to reproduce without dying.
There are things about ourselves that evolution did to us that we ought to change. Like dying of old age, for example. Evolution is not moral. It is indifferent. The Sequences illustrate this very clearly.
If it's worth saying, but not worth its own post, then it goes here.
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