His arguments were generally driven by logic and reason, not rationalization. Rationalization is generally only necessary for adopting views that seem ostensibly inappropriate, which would certainly include these sort of 'naturally repulsive' acts. And indeed his arguments for slavery were some of his weakest precisely because they were uncharacteristic rationalizations.

I completely agree that if you go back far enough in the evolutionary pipeline then my claim becomes invalid. I also think it would not apply to people of a sufficiently reduced IQ. You need to have a minimum of intelligence to understand what you're doing, alternatives, and its consequences on others. But once you have that baseline of IQ then I think morality, and a natural repulsion to certain behaviors, comes as naturally as communication.