I've been on Cipro for several years, with just a few pauses. Others prefer an antiobiotic rotation, if they have to stay on antibiotics to maintain good function. It's useful to have additional choices that work for you, but I wouldn't panic based on one bad day.

I've tried a few times to stop the antibiotics, but it just doesn't work for me, and I refuse to live that way (with uncontrolled pouchitis) as long as I have an alternative.

I'm wondering why your doctor hasn't had you try a different antibiotic because you are still having symptoms after taking it for so long.  I can't take Cipro because I got a c.diff infection from it years before my j-pouch surgeries. I'm telling you this because unlike Scott I can't take Cipro.  I have chronic pouchitis now and rotate between flagyl and augmentin. Cipro isn't the only antibiotic used. 

have you been able to lower your dosage?  I am on Flagyl (which is working for me) and I started at 550 mgs twice a day and now I am down to 325 mgs once a day.  And if all goes well to taper to zero but it's been a slow process.