J Pouch or Ostomy surgery is not a "cure" and is not designed to be, rather it is the elimination of all or part of an organ that is unable through treatment to cope with a disease process which has not left your body, that being autoimmune disorder. IBD is simply a manifestation of auto immune disorder (AID) which is systemic and not addressed by ANY surgery. AID may, and probably will, manifest in other ways during one's lifetime. In addition to IBD with my J Pouch, I was diagnosed with inflammatory airway disease 28 years after getting my J Pouch (non-allergic chronic rhinitis). I also have CSR, central seruos retinopathy, which is believed to possibly be caused by AID. Pouchitis, Cuffitis, Crohn's, rheumatoid arthritis, irisitis and other inflammatory conditions can manifest after surgery as a result of underlying AID.
The drugs that really treat the AID as opposed to the IBD are the biologics and immunosuppressive drugs. They treat the underlying disease rather than symptoms of the disease. Patient take Remicade for a wide assortment of autoimmune disorders, of which IBD is just one subset.
As opposed to a treatment plan, surgery is simply a stalling mechanism to halt the attack of AID on one part of your body so as to prevent further deterioration and/or death, allow healing and other methods of treatment. And it turns out that in some cases no further treatment is necessary, even though AID remains in the body. In those patients, they are not cured; their AID is simply in remission for the moment, and may or may not resurface later as Pouchitis, Crohn's or whatever else.