I think maybe after the biopsies come back you should have a talk with him about your concerns, after also getting your surgeon's take.
All of the GIs seem resistant about going to antibiotics until everything else has been proven to have failed. In my case they tried rectal meds, entocort, rowasa enemas and probiotics which all failed before I achieved great success with the rotating antibiotic regimen. They want to see a pattern of failure of other treatments before you are married to antibiotics like I have been for 17 years. And maybe those meds will work for you.