I would hope that at some point in the future, this would be the go-to treatment for all auto-immune disorders, because it makes a lot more sense than all these other immune suppressants, etc. But, Western medicine never ceases to amaze me... and I don't mean that in a good way.
As of now the treatment is still very new (only 15 years old) and there haven't been any major double blind studies (they are underway, but do not have results yet). So the newness factor, combined with the unappealing chemotherapy factor, would make it a last resort even from a patient's point of view.
I don't know the exact statistics on the risk factors involved in this treatment, but I do know they are minimal. The most dangerous thing in this situation would be an infection, or developing host v. graft disease, which I think is pretty rare. I think the most likely or most common downfall would be the donor stem cells not "winning out" when re-growing the immune system. Which means the patient's own body is re-growing the immune system. So there is a likelihood of the disease returning at some point, but most patients (myself included) feel that even five years free of this disease are well worth all the risks and expense. And when I say five years disease free... I think that is almost 'worst case scenario', at least for me. Majority of patients so far don't see a return of disease for 10-15 years, and for many the disease has not returned at all. But the really great thing is that if or when the disease comes back, all the medications and therapies that stopped working before will work again because you have a brand new immune system. It could probably even be controlled through diet and holistic approaches in most cases. But, I am not a medical professional and don't know the research front and back, so please, don't take my word for fact.
The transplant is very expensive. The big pharmaceutical companies cannot profit from this, so there is no one bankrolling the research and trials, making the process take longer and making it less accessible to patients because of cost. Also, many private insurance companies will not cover it, or at least put up quite a fight, taking months and months of repeated denials and appeals. The cost is approximately $125,000-175,000 from what I know. I don't think that includes travel and board expenses.
Your question about the immune system not restarting and being stuck with 0 is actually a very good question... I have no idea! I'm not sure if it's even possible. The biggest concerns in the screening process are: 1) Making sure that the patient is healthy enough to endure chemo. 2) Being certain that there are no existing or persistent infections in the patient's body that might cause a problem once the patient becomes neutropenic (sp?) or is without an immune system.
And your last question- The answer is that any patient being considered has to fit a certain criteria, as with all new treatments. Part of that criteria is trying and failing to respond to all 5-ASA medications, and failing to respond to at least two of the biologics (i.e.-Remicade, Humira, Cimzia, etc.). Also, you have to have been diagnosed with Crohn's disease for at least five years. Not sure the exact reasons behind these criteria but that's pretty much standard for any drug trial.
Hope that helps... my memory is terrible though, so if you want to do further research, send me a private message, and I could probably dig up a few sites for you. Also, if you look under Stem Cell in the treatment section of the forum you can find blogs from patients who have undergone the transplant, which is how I found out about it.