The Anime may try to act innocent but the world is more realistic than it gives itself credit for. Unless everyone in the world is a Vegetarian then yes they all eat Pokemon and Pokemon eat each other as well. The manga depicts the more mature nature of Pokemon much better.
When I'm Miqo'te http://www.youtube.com/watch?v=h3LGf9SSWrU
A berry takes 2 whole days to grow. we eat 3 times a day and the only thing I see is rocks, potions and pidgeys. What do you think i'm going to eat?
The pidgey of course.
Ever wonder why they're only one of each starter in the game? Cause they're being mass produced, slaughtered and canned for our consumption, the professor just takes one of each so that they wont get suspicious.