Many many people, whether it's parents with kids or adults trying this themselves, find that they are healthier when they go off milk and cheese. As a musician/singer, it's accepted that "loose dairy" is associated with mucous production, so singers tend to avoid milk and cheese before performances to keep the phlegm down. And as someone who is milk-protein-intolerant myself (our whole family is), there are absolutely positively intestinal/digestive effects from MPI.
There could absolutely be an allergy or at least an intolerance there that might be worth avoiding diary for, at least in its raw forms. I know some people who heat the milk to about 180F and then let it cool for drinking; if you really want him to have it, that might be worth trying. Here the only dairy we can tolerate is yogurt (and sour cream), so I make a gallon of yogurt a week out of full-fat milk.
BTW, many people with dairy issues also have similar problems with soy; I've read that the proteins are similar enough that in some cases the body reacts the same way, so soy milk may not be a good alternative option.
