Crohn's Disease and Flagyl

I recently had a colonoscopy and had a polyp removed in the bowel area. In addition , I had a biopsy in the tranverse area of small intestine . Both were normal , but the Doctor found a fistula and prescribed a regimen of over 200 count Flagyl. I have been experiencing numerous side effects which are very dibilitating. I am constantly on the toilet and feel like vomiting ALL the time . Is the doseage a bit too much ? I cannot imagine taking this drug another two months , especially when I am only three days into the treatment with these kinds of problems. I understand Flagyl is a strongrer than normal antibiotic and do not understand why it should take two plus months to treat this fistula . Please comment and also suggest an alternative ( if one exists).