I also have a chondral flap.
Lots of people have rents in their chondral cartiledge. The way to fix that is to allow it to heal by diminishing the ground reaction forces that stress the knee joint (ie: stop running with a heavy heel strike).
The studies on barefoot running are impressive with regard to the diminished forces at the knee and hip. The problem is that SOMETHING has to absorb the force. When running barefoot (or with little to no hindfoot support) the forces are absorbed by the muscles and tendons that surround the ankle. We are talking about momentary forces of 5-10X body weight. It takes a long time to have your tendons adapt to that kind of stress. Slow and steady is the only way to accomplish this.
Your orthopedist is wrong. We are born to run (cue "The Boss"). Just not with shock absorbing running shoes.
Jen, I am the perfect example of this. For the past 30 yrs I have believed that I could not run. Because since I effed up my knee, every time I would run, it would swell up like a grapefruit and hurt for 2 weeks (I destroyed my medial meniscus, needed a repair of the MCL and LCL. I now have moderate medial joint space narrowing, ie. osteoarthritis). I have NO knee pain when running now. But despite running 3-4 d/wk, I am stuck right at 6k. Any more than that, my ankles kill me. I am doing this with the plan of increasing my distance over the next 2-3 years.