I have had Pouchitis for 25 years and never was prescribed Vancomycin by anyone.
The leading Pouchitis treatment antibiotics are Cipro, Flagyl, Xifaxin, Augmentin, Levacquin, and Tinidazole. You would have to ask your doctor why he is using that particular antibiotic which is more of a go to treatment for C Diff, from what I know.
Of course you may or may not have side effects with the others as well, but they are known to be effective treatments.
If antibiotics don’t do the job, you will be a candidate for biological drugs, and if your inflammation is characterized as “severe” that could be sooner rather than later. Antibiotics can sometimes help with the symptoms, while not totally improving the level of inflammation, and you should be cognizant of this. That’s why you should have a conversation about biologics. You don’t want the inflammation to not be under control.