Hey, S.!
I'm doing some research on this for my friend too, I don't know yet. You have gotten some awesome info and responses I'm going to use.
I almost had to take my doctor's orders to take my daughter off milk because she had bad eczema as soon as I stopped nursing and gave her milk.
I didn't (luckily, it passed six months later even with milk still in her diet) because I couldn't figure out any way to replace that much calcium AND D and nutrients and protein and MOST of all the essential fat for brain development. I'm not sure how well supplements and enriching soy etc actually works since they're engineered and not directly from a food source. (I'm no doctor, or nutrition specialist, I just don't always believe labels). Some veggies have calcium, but its not easy to feed a baby more than a few servings of veggies a day-and veggies don't have the fat.
Now they're finding out that lactose intolerance is highly over diagnosed and lots of kids are lacking the fats etc in milk that they need for their brains. If your daughter has a healthy diet, there is not a whole lot of other good fat to compensate. Vegans would disagree, so maybe check their sites on baby nutrition, but don't forget the fat, not just the calcium!
My friend's son is truly allergic, so we're looking for replacements, I'll keep you posted, but until you're confident you've found all the replacements-TRY really hard to get her drink her milk! Or eat even more yogurt per day, smoothies etc. Maybe there is an organic un-sugary way to flavor some milk..cheese raviolis...parmesan is high in nutrients..be sure to get plenty of olive oil, nuts, avocado and other natural fats in there! Would you be able to smuggle fish oil into the picture? Not easy, I've tried. Good luck!