My children have cow's milk allergies and are also allergic to soy milk. We used rice milk, but had the same concerns regarding necessary fat (& protein) for development. We now use goat milk and rice milk. My kids under 5 get goat milk almost exclusively and the older kids have it whenever they want. Myself and my 11-year old girl prefer the rice milk. I do use goat milk in cooking, though. It works much better than the rice milk! It is expensive- we dilute ours with water in equal parts. Goat milk is also fattier than cow's milk. It's usually around 4-5% fat, so mixing it with equal parts water gets it to about 2%. Hopefully your kids can do goat milk. The canned stuff is nasty, but you can probably find some regular goat milk in a carton at your grocery store or health food store.
If they can't do goat milk- look into fatty natural foods. Avocados, olive oil, other oils, meats, nuts (later), etc.. Did you nurse her or use something else? There's no need to start whole milk if there are allergies, you can still use whatever you were before, and start adding in the regular foods.