How long has it been since you stopped BFing? If he is "milk intolerant" it is likely dairy milk IN your milk, not YOUR milk in particular. It makes me mad when doctors take babies off of something so natural and healthy when there is in theory an "easy" fix (not easy for mama, but simple). I am in the process of switching peds and her philosophy regarding my children and dairy is one of the #1 reasons why - no matter how many times I have said my children are sensitive to dairy she insists I force feed them whole milk throughout the day. She scoffed when I said I went dairy free while nursing DD and insisted dairy sensitivities are rare - soooo NOT true! She wanted me to put her on a high powered reflux med instead. Turns out, she was fine after cutting dairy out of my diet completely. I wish I would have known the same for DS... I honestly believe he would be a different child today had I done things differently.
Anyway, many times if a child has a dairy sensitivity, soy can also be an issue so soy formula won't help at all. If it hasn't been long since you stopped nursing, there is a chance you can get your milk going again with some higher doses of fenugreek and some other things (contact an all natural lactation consultant and they can help). I know one lady who was semi-successful even after months of not nursing!
IF, big if, you are able to start nursing again, cut dairy our of your diet completely... read every label - no milk, butter milk, whey, etc. Nothing. It's tough, very very tough. Dairy is one of my main food groups, and I successfully did it for 6 months or so which gave her a chance to grow out of it. I was able to slowly incorporate it back into my diet (she nursed for 14 months or so) and she's fine with it now. One positive outcome for me was dropping post baby pounds like crazy! ;) It takes about 2 full weeks to get it out of your system, but the results might be miraculous like it was for my DD. She was easily able to go off all reflux meds and was a happy, peaceful baby (very much unlike my son). We've also had a lot fewer health issues with her which might be coincidence, might not be.
Sorry for the novel, this is just one of those issues I am pretty "passionate" about... I hate seeing babies suffer b/c of doctors ill advice when all other avenues have not been taken. It's just easier to write a prescription or switch to another formula (not matter how much the cost is to you!) rather than to truly listen to the parents and see what other options there might be.
Getting off my soapbox now...