Some Moms use goats milk.
Yes, I would stay away from Soy milk, lots of contraindications on it. It's not a myth.
For me, as a child, I ate like your son... the reason being that because I ate so naturally and healthily and home-made...my body basically rejected anything "processed" or off a shelf or already prepared. I would get migraines and stomach cramps from anything that was "not" home-made. I gradually grew out of it as I got older in grade school. So maybe this is the case with your son. It was for me. Needless to say, my Parents were always so impressed with me and the way I naturally ate so healthily... but there was no other way, since my body reacted negatively from anything non-home-made. It was just a natural inclination of mine...I was like that since I was very young. Although I could drink milk.
Depending how old your child is... the "whole milk" is for the milk "fats" which is essential for brain development, and the calcium and vitamin D. Perhaps, you can give him supplements? Check with your Doctor. It's always good to continue taking "Omega-3" vitamins/supplements... this also is essential for brain/neurological development and is good for kids and adults.
Good luck,
Susan