I waited 3 1/2 years with chronic pouchitis before having the pouch out. Antibiotics CAN be harmful, but its a risk reward problem. If you are okay with the potential risks and they make you better, then great. After 3 1/2 years on antibiotics I still had a subpar quality of life. I saw four surgeons about pouch removal and 3 claimed they could fix it. But I was done. I didn't want to waste more of my life on trying yet one more thing. I felt like I had done enough and just wanted to move on. Everyone hits that point at a different time, some never hit it. Some would prefer to do anything and everything to make the j-pouch work. Any of these is fine choices, its all about what you want, what you are willing to do and in what time frame.
I was in my early 30s and wanted to have babies. I didn't have a lot of time to wait for something to work, and I didn't want to risk my future fertility with a lot of surgeries to fix something I was perfectly fine getting rid of...Pouch removed in 2003 - no GI issues, no drugs, no diet restrictions AND - two beautiful children now almost 10 and 7 1/2. It was the right call for me. Wish I had done it sooner.
Jill