Yep, chondromalacia for me also. 4 knee operations when I fell backpacking and turned a chronic problem into acute with a tear on my kneecap. Did your doc talk to you about prescription orthotics? These can help align your knees. Without these, I wouldn't be doing anything active. Might be worth a little research. If you go this route, be sure to find a sports med podiatrist who works with cyclists so that he/she can fit the orthotic in your cycling shoe.

Clipless pedals help because I can pull up. The pushing down for hills can be a killer and strength is a critical factor.

Chrondromalacia for me means no tennis or volleyball any longer.