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Interesting question. My understanding is that the homogenization process is almost like a second pasteurization. The resultant small fat particles are prone to penetrate the gut wall ( I think... shall have to google some references). I've started buying unhomogenized milk and mixing it 50-50. I don't use much dairy at all myself now though.
Since I don't think that you can get homogenized raw milk, it wouldn't be the homogenization that would bother me so much as the pasteurization. If you're going to drink milk, you should have the bacteria in your gut that will help you break it down and digest it which you're only going to get from raw milk. http://www.realmilk.com/ has a lot of really good information about both pasteurized milk and raw milk. The powerpoint presentation they have down about the middle of the page has TONS of really good info in it.