I just discovered something that may be useful to you. Medifast posts official allergen information
here
This document lists which of their products do not contain which common allergens. And yes, they do have products that do not contain soy. So if the problem is soy, it still may be possible to continue on Medifast (but with a much more limited menu.)
It's also possible the problem ISN'T soy, but is one of the other common allergens. In that case, this list may help you avoid those as well. That's why I was suggesting allergy testing.
Allergy testing is subject to a lot of false positives, but it's much more accurate if you're trying to confirm an allergy for a specific allergen. And while your regular doctor can conduct allergy tests, you get better results with a specialist (because of those false positives.) We recently had allergy testing experiences with one of my kids.