I had a really bad case of Crohn's Disease and ended up having a proctocolectomy, which is where they remove the entire colon and rectum. I have a permanent ileostomy and haven't had any health problems since my surgery, so I definitely don't regret having it done.
I hope that your wife's surgery is a success and that it takes care of her colonic inertia. Please keep us posted on how she's doing after surgery. You are both in my thoughts and prayers.
Dx'd Crohn's in '99 at 28. Proctocolectomy & ileostomy in '06.
Pain-free, med-free, and very thankful to be healthy again :)