How can we decide at which level does natural selection apply?
Natural selection favors genotypes that produce phenotypes that survive to reproduce.  To the extent that natural selection drives the instincts that drive predation, the (essentially tautological) answer is that, "It has proven selectively beneficial for that particular genotype to eat whatever it's eating."

Indeed, nature has shown us a variety of solutions to these selective pressures.  Cannibalism is not hard to find.  In the extreme case, mothers from diverse species are known to kill and eat their own offspring, which at first glance may seem like the height of failure when it comes to propagating one's genes.  And yet we can hypothesize a number of selective advantages of that behavior.  (E.g., the mother can produce large litters when food is plentiful, and then adjust for shortages to shore up a smaller litter when food is scarce.)

We also know that there are selective pressures against eating similar animals.  For example, pathogens that kill an animal are likely to afflict its genetic relatives, and so that could drive the aversion of some carnivores (including humans) to eating close relatives.

There are plenty of examples of evolved symbiotic organisms.  Alligators don't eat plovers, and sharks don't eat remoras.

But it is hard to imagine selective pressure for altruistic behaviors that don't benefit a particular genotype.  E.g., if there are mammals to be eaten, the lions that eat them will survive and the ones that don't will die.  If the entire class Mammalia is under pressure, population dynamics trump evolved behavior: If prey become scarce, predators will become scarce.  But if any predators survive, it will be the greedy ones.