If it's an allergy (not an intolerance), you can go for testing. They can do a blood test (RAST) and skin prick test (SPT) and let you know if she is allergic to milk, soy, and a host of other foods.
If those tests come back negative, you have an intolerance on your hand - which most babies outgrow by 18-24 months (if not sooner). In that case, you might want to wait until it's been 3 months since you last pulled the dairy and soy and try again slowly - with hidden dairy and soy first and then slowly moving on to cheese, etc before milk.
Have you tried rice milk? Not much fat but plenty of calcium and you can get fat from other sources.