M.R.
Our family doesn't have allergies but we are mostly on a soy diet. Our 22 month old is also drinking soy milk and eating soy yogurt. I cleared this with our pediatrician and she had no issues about the lack of dairy in her diet. She's been on soy milk since we stopped nursing. I do recommend the Organic Valley soy milk over the Silk. The Organic Valley has a creamer taste and is less "soy" tasting. And after taste testing many, many soy yogurt brands we found that Whole Soy & Co is one of the best. My daughter just loves the mango flavored one. And we haven't tried the soy cheese yet (it's our only dairy weekness) but I have heard good things. All of these items can be found at Whole Foods or Vitamin Cottage. Oh and as a special treat, my husband and daughter just love the spray soy whipped cream in the can. Can recall the name of it but it is carried at the Vitamin Cottage. They also have many varieties of soy and rice milk ice cream, all are tasty.
As for cooking it in your food...anything that calls for cheese, maybe you can mix it in after you've finished. That way if you don't care for the soy cheese/milk you can mix in the traditional cheese.
It is a transition but it's fun to experiment and your daughter will surely appreciate your efforts :) Good luck :)