I think the treatment is in no way going to get rid of it. Did he tell you that you must clean like crazy? That one cyst can reinfect? I think I would try to find another dr. I found this link for you that you can read over too
ACVC 2001 - Diarrhea Caused by Giardia and Clostridium Perfringens Enterotoxicosis I would suggest the use of panacur, but I am not a vet!