From a rather uninformed novice, my knees feel subjectively healthier since I started riding fixed. I don't skid or back pedal hard, but I do back pedal lightly to control and regulate my speed on gentle slopes or in the run up to a full stop. After an initial increase in pain for the first week, my long-standing (2 years +) knee pain has actually decreased. I think this kind of eccentric work is quite beneficial for you.