I was raised on soy back in the day it was all they had other then breast milk and cows milk. And I am just fine.
I have 2 wonderful girls who were also raised on soy formula and soy milk! I also used lactose free milk that is rbest free due to the actually scientific proof it can harm young kids.
I also had one of my kids for health reasons who is growth hormone deficient (she was born with a tiny pituitary gland we found out at age 1 yr and they said it was due to her medical conditions not soy. ) on soy formula tell age 2 1/2. Shes just fine no boobies nothing, hell she didn't get HAIR until we started growth hormone shots. ( We choose to wait tell age 2 1/2 yrs to do this due to the negative stuff from those.) So yes soy is fine for a boy, as my brother was raised too on soy and hes 28 married and no bobbies either. Some kids yes cant have soy or shouldn't from a medical point of view but if his dr who has taken care of him it sounds great if he was able to diagnose the things you say in the about me, then he should know. But if the dr says not to then listen. Like if it aint broken why fix it? :)
But I do understand how you could be concerned but I would ask his dr if I were you. And research it threw the sites.
I also used with my kids the silk fortified very vanilla soy milk when they want it now. And I asked my other lactose intolerant daughters dr about it he said he if she will drink it honestly its better for her in moderation for extra vitamins and I make them both smoothies with it and they love it I also add protein powder (dr asked me to, to replace the lost proteins from soy.) and they dont notice it. (I think this is why, http://www.soyonlineservice.co.nz/)
But ultimately its your choice do you wanna continue and give him the soy or change to something else. Just do your research with REAL scientific facts is all I ask.
I hope this helps, also try this site (http://www.westonaprice.org/splash_2.htm)
Also organic is nice but really its not much better or worse. Maybe in some things like veggies (pesticides.) or milk (cows and growth hormones and bad feed.) and so on. Soy beans are your least worry when you think about it. Hell even meat can be bad due to what farmers give the cows now. (personal opinion.)
Other options if you choose not to use soy -
http://www.sixwise.com/newsletters/05/08/17/soy-milk-rice...
http://www.natural-family.com/3nut-62-soy-milk-alternativ...