Chondromalacia isn't really a diagnosis, it is more like a symptom of things not tracking properly in the knee, thereby causing irritation and wear behind the patella. Like weirdknees said, there can be many different causes for the tracking issue. Taking the conservative approach is a good idea, to see if things can be gotten under control. Emphasis on strengthening of the quads, hamstrings, glutes, calves, and hip muscles is a good idea, along with stretching. You can start with isometric exercises like quad sets, straight leg raises, hamstring curls, etc and then progress to weight bearing ones like wall squats, leg press, etc as pain permits.
The stationary bike is a good tool for this endeavor. Shoot for one hour a day at your target heart rate.