If you're talking about the A1/A2 proteins, then goat does not have the "bad" protein. I can tolerate goat milk and I drink a lot of it, while I cannot touch cow's. I can't even touch the raw cow milk with the "good" protein in it.
This thread handles the topic fairly comprehensively: http://paleohacks.com/questions/62635/goat-milk-instead-of-cow
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