I felt like this draft paper by Anders Sandberg was a well-thought-out essay on the morality of experiments on brain emulations. Is there anything you disagree with here, or think he should handle differently?
http://www.aleph.se/papers/Ethics%20of%20brain%20emulations%20draft.pdf
The problem is that food scales. If you do animal research, you're causing distress to the animals, but it's constant. It doesn't matter if there's one person or billions. You only have to do the research once. Food isn't like that. If you want to feed a billion people, it requires a billion times more animal cruelty than feeding one person.
I guess what I tried to say is that cruelty isn't necessary for growing animals for food, but it is necessary for certain kinds of research.