If all animals are “inherent and natural” slaves to humanity, then some of them are pretty damn poorly equipped for the part. Take cats, for example. Some anthropologists might tell you that they were domesticated to control rodents (the cats, that is, not the anthropologists); however, they have since clearly been outevolved by the spring-loaded rat trap, and yet they really don’t seem too motivated to pick up any other useful skills. The octopus is another good example–smart though they may be, what good is it to have a slave that dehydrates on its way to get you a beer? Good luck getting a brown hyena or a water mocassin to show you proper obesiance, either. Generally speaking, animals make lousy slaves.
A certain degree of moral dissonance toward the animal kingdom is essential for survival, even if you’re a Jainist monk or something. If you don’t draw the line between humans and other organisms, there’s really no good reason to draw it anywhere else, and soon you’re agonizing over the injustice of digesting your own intestinal microbes. On the other hand, if there’s a way to minimize the suffering of animals in a way that doesn’t adversely affect their flavor, then I’m all for it.
As far as superintelligent mutants or aliens go, well… I think it’s helpful to bear in mind that for the most part, use of animals tends to drop away as soon as there’s a way to do the same job as well or better by other means. In industrialized nations, we no longer rely on horses for plowing or transportation, we don’t use whale-oil lamps anymore, and I’m sure that factory farms will start to decline soon after we figure out how to grow a Porterhouse steak in a tank. Medical research is the same way; animals aren’t used by choice. They’re messy, expensive, and require a lot of care. But at the moment we don’t have any non-animal models that can give us an idea how a given treatment is going to affect the whole organism. If there were a computer program that could reliably simulate all the variables of a biological system, no doubt researchers would be overjoyed not to have to smell like mouse urine anymore.
All of which is to say, if super-advanced aliens show up, and they think anything like the way we do, they’ll have even less reason to enslave us than we have to enslave each other. Yeah, they may have some sort of freaky desire to hunt us for sport, but it’s not like we’re going to say, “Ah, well, we humans have hunted less intelligent creatures for millennia, and now, seemingly, the worm has turned! How ironic! What a Serlingesque turn of affairs, that our species should recieve such a comeuppance!” Hell no, that’s when we break out the action heroes and 50’s-era tweed-jacketed scientists.