Here's an abstract about 5 Crohn's patients who underwent allogenic transplant. 1 relapsed after 1.5 years because their transplant was mixed chimerism. The others have had no symptoms of cancer of Crohn's for years after the transplant.
Kasper, the immune system is destroyed by high doses of chemotherapy. Then the donor's stem cells are infused into the patient. Since stem cells go to the area in the body where there's damage, in this case, they detect the lack of immune system, and basically grow a new one.
There's obviously a risk to getting someone else's immune system. That's why the donor is usually a brother or sister who is healthy. However, you never know what diseases they're predisposed to.
I read one article about a person who had a transplant for leukemia. The donor had Crohn's and so the Leukemia patient eventually developed Crohn's as well. This is why people with autoimmune diseases are not allowed to donate bone marrow.