You're arguing from a perspective of nature. The OP is arguing from one of morality. Morality is antithetical to primal instinct, because humans have developed a level of autonomy and understanding of the world beyond the primordial wilderness. We don't need to eat meat to sustain ourselves, and the tools and infrastructure we use to facilitate flesh consumption is far from natural, unsustainable and often extremely cruel.
If society were about implementing laws based of natural impulses, killing other humans and rape would be permitted. Instead society is about instilling a system of morals and enforcing they're not breached. If the cruelty and killing of animals is protected why shouldn't sex with them be ?