I agree with Sannah. I have gluten intolerance. A recent Finnish study showed if someone is Celiac (the hereditary, autoimmune disease of gluten intolerance) and he/she eats less than a teaspoon, 30 mg, of cake, it could be damaging to their digestive tract. This may be the same for other food allergies, I don't know.
Maybe think of food allergies like smoking... cilia of smokers' throats become paralysized as they inhale toxins. Eventually the cilia die...creating new problems, like emphysema. In my mind, food allergies act in a similar manner. A food that our bodies cannot tolerate is harsh on its system, so may damage the villi of the small intestine (just like the cilia in smokers esophagus), for example in Celiacs. I don't know what type of food allergy you have but as far as I know you cannot alter your body. I would love if I could eat gluten again, but in most cases, a food allergy means a lifestyle alteration. The good new is it gets easier with time... Good luck!