@firstviolin -- You're right, that is a major concern with elemental diets. However, most of the time a person is only put on an elemental diet as a last resort, or when their illness becomes so serious that normal digestion is simply unfeasible, or even painful.
However, most people who are put on a Crohn's diet or IBD diet are put on it by a doctor or nutritionist who is trained to make sure that they get all the nutrition that they need during the period that they're on the diet.
Also, many companies offer premixed elemental diet formulas, some of which come with protein powder mixed in, which can be a good option for people who need to be on an elemental diet for a longer period of time, and are not allergic to the types of protein found in the formula.
So although you do pose a very major concern that many people have when going on an elemental diet, for the most part, the doctors can offset that as long as the person is not on the diet for too long.
Hope that helps!