In the episode with Bill the Pokemaniac from Season One, Brock offered to make some Cheeseburgers for lunch. And also, in Gold/Silver/HeartGold/SoulSilver, if you try to touch the sink/stove/whatever, it mentions that your mom is making cheeseburgers as well?
Here is what I know. Pokemon are the same as animals in our world. Humans are also Pokemon in the game world, just like they are animals in our world. So for a Human to eat a Pokemon is no different that for a human to eat a cow
I guess the Anime doesn't adress this question since it's a kid's show, but i'm pretty sure that Pokemon eat other Pokemon, as well as Humans eat Pokemon too. It's just the circle of life, and since Pokemon are the "animals" of the pokemon world, there also has to be a food-chain of some sort.