So are you against killing rats, ants, or flies because that violates their autonomy?
It's a gradient, morality isn't black and white. Stealing isn't quite as wrong as killing, but they're both wrong, right?
The same applies to killing animals. Killing human beings is worse than killing a cow because humans have a higher degree of autonomy than any other mammal (in all likelihood). Killing a cow is worse than killing an ant.
I don't mind swatting flies because the degree of autonomy and "choice" that insects have is probably negligible, so I can't bother myself with them.
It's like the word "adult." We know that a 4 year old isn't an adult, and a 60 year old is. But the line in between is always going to be arbitrary. That doesn't mean that, because there is arbitrariness, that we should throw away the entire thing altogether.
Killing cows, in my opinion, is definitely wrong. Ants, eh, not so much. And that's directly a result of the core of what makes something right or wrong, which I believe to be the restriction of autonomy.
Have you asked a cow what they want to do and have they ever told you that they don't want to be safe from predators and have a steady supply of food and water? I possibly might need to defer this question to mpbiz, since after all he is the communications expert.
Have you ever been in a slaughterhouse and seen the reaction of pigs as they're let off the truck and they hear the squeals of other pigs being slaughtered? They're not exactly itching to go in.