Exercise Leading to Knee Problems

I was weighing 118 KGs in March 2009 when I started the weight loss routine with restrictive diet and exercise. By September 2009, I had reduced to 99 KGs. For exercise, I started with 2 KM walk in March 2009 and increased to 2 KM walk and 2.5 KM of running everyday by April 2009. It went off fine till November when the left knee started giving problem and I felt pain in the left knee while running and climbing stairs. I am 41 years old. The CT scan revealed bone marrow swelling with a blunt injury kind of impression. Soon the pain became so severe despite medication including steroids, that I had to stop the exercise. And with that the whole motivation to reduce weight was also lost. I started eating badly again and am now back to 109 KGs in nine months (after I stopped exercise). The doctor has advised that I should refrain from running and do very slow walking if I feel like. But I want to come back to the exercise routine. Is there a way I can do that now? Any diet which will help me handle this. The orthopedic says that surgery on the knee is not possible till the bone marrow swelling goes.