She has been through a lot. Try mixing powdered Instant breakfast, chocolate milk is better then none. I think all kids go through milk strikes with NOTHING to do with allergy relations. I think it is normal. Both of mine did and then went back to drinking it again.
Give her yogurt, cheese, calcium enriched juice (one cup a day), even tums has calcium. What she gets from milk is Vitamin D and calcium one she can get from sunshine and the other in tons of different foods. Even in her cereal that is great! Get the strawed bowls and maybe she will drink up the leftover milk in the bowl.
Give it some time, just offer it in different forms and let it go, otherwise it is a power struggle. Try strawed cups too, my kids LOVED drinking from those.
Hang in there, she will drink it again, the Dr is right to have her stay hydrated and eat balanced foods vs worrying to much about milk.