Ethics. Either you believe it's perfectly fine to advise other humans to eat a deficient diet, or you believe it's perfectly fine to eat animal flesh yourself. Once you made up your mind on that, how your food-animals are killed makes no difference. Having said that, an animal that is killed quickly and painlessly tastes better.

It's not a question of whether we will kill the animals or not. That has already been decided: We will kill the animals. Rather, it's a question of how we will kill it for it to become the best food for us.