I doubt 70% of human population is allergic to milk. If you just read Wikipedia article about milk allergy you'll find out that the rate is 3% and 15% of those 3% are also allergic to soy. And that is just about children. Only 0.4% retain milk allergy in adulthood.
I can imagine that 65% people don't have ability to digest lactose because they lost it at some point because of culture and food availability they didn't need to retain it beyond childhood.
The funny thing is that the problem is with just lactose and if you supplement the missing enzyme nearly all people can draw nutritional benefit from milks vitamins, micro elements, sugars and fats.
Could you point me to some research indicating superiority of soy milk over any animal milk, preferably one that's not analogous to "eating Teflon is healthier than eating a burger for the purposes of weight loss"?
Also, 70% of the human population is allergic to cow milk (as opposed to 0.4% being allergic to soy).
Anyway, there's tons of data public about it that you can easily find, just wanted to respond to your "millions of years" argument.