Patients sometimes die from these types of transplants because it is often a very drastic procedure. You basically wipe out the patients' immune system with powerful drugs or high doses of radiation (or both) and then replace it with a new one that develops from the injected stem cells. After the old immune system is destroyed there is often a risky "hold on to your hat" phase while waiting for the new immune system to take hold and grow. The patient is highly vulnerable to infection during that phase. Plus the whole thing is just a big procedure with lots of stress on the body. That's why it is generally used only for diseases that are likely to kill the patient anyway if left unchecked - such as leukemia and lymphoma and some other cancers. For them it is worth the risk. But since all but the most severe cases of Crohn's can be controlled in less risky ways, and Crohn's is very seldom fatal, I think stem cell transplant is unlikely become widespread for treating Crohn's.