An appeal to nature is only wrong if it's saying something is good because it happens in nature. I don't believe I did so, except maybe saying it's ethically better for them to live in nature than in slaughter houses. I'd love to see an argument in favor of horrible large-scale animal raising though. That'd be interesting.
It being evolutionarily necessary isn't an appeal to nature. It's just stating a fact. It isn't a judgment. It's just a statement that overpopulation causes massive issues, and prey animals evolve to have tons of children because they were hunted (by other animals than humans) . Without hunting of some kind, their populations balloon out of control.
It's not circular, because it needs to be done. If it isn't done we have massive problems. It doesn't depend on any other logic. Sure, the issue was created, in part, by hunting also (a lot just because predators won't live near population centers though), but the argument that it needs to be done isn't dependent on you agreeing with killing predators.