The doc has you on the right path. If it’s diversion pouchitis then the best treatment is takedown. If it seems to be IBD-caused inflammation, then getting that controlled with medication before takedown will give you a better result. The biopsies aren’t perfect at telling these two different conditions apart, but they give you better information than you would have otherwise.
I had a fair risk of Crohn’s before surgery, and it’s never been ruled out. Pouch failure is more common in Crohn’s than UC, but I’ve been pleased with my J-pouch for about 17 years.