R., your doc could be right, but he/she could be wrong. I was told "not to worry about it" and my daughter, who was allergy prone by genetics, ended up having problems. Later pediatricians told me it DID matter what I put through my breast milk. Even if your doc is right, it can't hurt to try removing the soy protein from your own diet and see what happens. Soy is in the peanut family, and peanuts are a big allergen for babies. If that doesn't work, try removing other things from your diet, or take the time to do the non-allergenic diet thing, where you basically start with rice, chicken, green beans, applesauce, bananas and add in a food every three or four days, to see what happens to your son.
If you need protein, try Rice protein. I use and prefer it. My daughter, who had dairy, egg, citrus and nut allergies from infancy on, highly preferred the rice products (milk, ice cream, etc) over the soy products anyway.
Good luck to you. I know it's distressing.