I am glad to know that your surgeon is using a non-surgical treatment to correct the problem with your pouch. In my way of thinking, one should take advantage of other treatments before committing to removal of their J pouch. In my case, my pouch could not be saved due to dysplasia that would turn to cancer in a relatively short time. In mentioning an ileostomy, your surgeon is preparing you for the possibility that your J pouch may have to be removed, or the possibility of a temporary ileostomy to allow your pouch time to heal. My surgeon at Mayo Clinic offered me only an end ileostomy, but I wanted an outcome that would afford me with the best quality of life, which I felt the ileostomy would not.
You are fortunate to have the time to learn more about the potential options if your pouch cannot be saved. These would be the end ileostomy, the Koch pouch and the BCIR (Barnett Continent Intestinal Reservoir). If the time comes to make a decision about one of these options, you should feel comfortable with it. I elected to have a BCIR and am now seven months post-op and doing very well with it. This was the best decision for me. I can fully understand your anxiety about this situation, having been there myself. Please feel to contact me by PM if you wish, and best of luck!