I'm not in the same scenario, but I've had a doctor tell me to stop running before.

I ran a few races over the past few years, marathon and half marathon distance and after finishing the races I always had pain in my right knee. After last October, this pain lasted for 2 months so I finally saw my doctor about it. He thought I wore down my cartilage or hurt my meniscus. I ended up getting an MRI and seeing an orthopedic surgeon. The guy didn't even look at my MRI results just took x-rays and then told me that I'll probably have arthritis one day. He said I should stop doing all load bearing exercises(squats/deadlifts/leg press) and I should limit my runs to a few times a week, short distances and an easy pace so it feels like "you're not trying very hard".

After wasting my money with these guys, I finally went to see a sports doctor who came recommended from a co-worker. This guy was the real deal, he did a muscle evaluation, asked about my past history in sports, injuries diet, exercise and everything in between. He determined that my foot was hyper mobile which means it doesn't stop rotating and this causes my knee to try to overcompensate by hinging side to side instead of just front/back. This also caused an entire muscle imbalance on my right side of my body from my lower legs to my lower back.

He put me on a strength program and I got some custom orthotics for my shoes and I've never felt better in my life.

All that being said, your situation is different. You have a known medical condition. However, I would still highly recommend seeing a sports doctor who takes a holistic approach to treating you. Chances are, the new doctor will work with you and your existing specialist to come up with a plan that might let you run more than he originally recommended.

Good luck, hope it works out.