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
Also, saying something is evil doesn't mean it's not a necessary evil.
I think animal research has more potential to make the animals suffer than growing them for food, if both try to minimize suffering and other things are equal. Of course, the sheer difference in scope means more suffering will happen in food industry by incompetence than in research by intention.
The vast majority of animals being raised for food aren't in environments that try to minimize suffering even slightly.