there was a guy on BF a couple months back that started a thread about his knee problems. I am not sure what caused them specifically, but I do remember him saying he got help from his neighbor and fixed his knees by dropping his gear ratio down to like 55 gi and learning how to spin more. He slowly brought his gear ratio back up to something more normal around 70 gi and buy the time he had (not sure how long it was, but it was a while) his knees had recovered.

My theory on it is that if you ride an appropriate gear ratio, then resisting the pedals is just another form of building muscle. It will build up the muscles around your knee and actually protect your knees over time, not harm them. You simply need to be careful not to put too much pressure on them before the muscle is built, that is when you cause injury