It's a pretty cool idea. Although it's a tad simplistic way to consider the immune system, our bodies mount two types of responses: Th1 and Th2. Th1 favors our immune cells directly killing our own cells and baddies. Th2 favors our immune cells producing lots of antibodies which then tag baddies for destruction.

In Crohn's disease, our bodies, for whatever reason, seem to be skewed towards producing a really unnecessary Th1 response in the gut which causes our bodies to self-destruct the GI tract. By giving hookworms to a patient, the hope is that the needed worm-killing Th2 response (worms are too big for really an effective Th1 response and need to be coated in antibodies and essentially repeatedly nuked with cytotoxic chemicals) will shift the balance in the patient's gut from Th1 towards Th2, thus eliminating their Crohn's manifestations and symptoms. Really cool idea.