Well, I actually spent several hours last night researching this and reading a bunch of stuff, and stumbled across this piece:
The Clinical Assessment, Treatment, and Prevention of Lyme Disease, Human Granulocytic Anaplasmosis, and Babesiosis: Clinical Practice Guidelines by the Infectious Diseases Society of America which looks to be a pretty thorough piece on the treatment of the disease. Seems my doc is following their guidelines to the letter.
This study concludes that better results were not found given higher doses and longer duration of antibiotic treatments. It appears from my reading that this is the mainstream medical opinion, and that the groups referenced in the links provided by Dean are more fringe elements. Which I guess isn't to say they are wrong, but they are certainly the minority opinion.
In any case, now I've read both sides of the story. so the doc and I have a good chat about the course of treatment. And everyone is in agreement that the blood tests are not reliable, so I'm sticking to the treatment even if today's result is negative.