I think recent studies don't support the idea that running destroys your knees, actually.
Distance running tends to increase surface area of knee cartilage. Lifting weights seems to increase thickness of cartilage.
However, thickness of cartilage seems to have a maximum value beyond which it will not increase. This may be because the chondocytes (cells inside the cartilage that produce and maintain it) gain all their nutrition by diffusion, so cartilage that is too thick would prevent adequate nutrition.
Lack of activity certainly leads to reduction in cartilage thickness, possibly surface area. It is unclear how exercise should be prescribed to optimally restore this.
Irregularities in cartilage surface, due to injury or possibly genetic bad luck, can produce irregular pressure on the underlying bone surface. This seems to be a driving factor in bone changes in early osteoarthritis.
Everyone's response to exercise is unique to them. It's not currently easy to say whether distance running is "good for you". However, the benefits of exercise generally outweigh the risks. Personally I suspect that only a tiny minority of people are capable of regularly running marathon distances and benefiting from that.
If you are over 40, don't expect to do then save intensity or duration of your younger peers, particularly if you are starting a new form of exercise. Your body has already adapted to your lifestyle, and it will be slower to adapt. But find what works for you, do what feels good, don't compare yourself to others, and enjoy yourself.
That sounds good and right, especially 'don't compare yourself to others'. It is a good Zen training to let others go faster and stick to ones own goals.
Daniel Lieberman (Harvard professor) has excellent research on the subject for those interested.
By the way, have you eliminated the possibility of compartment syndrome?
The reason I quit training was because a guy in my track group had the same problem and he didn't quit. It resulted in a badly fractured ankle which took him out for a whole season. I hadn't met him before (I was new to the group) but he turned up to training one day to say hi and told me his story which was a bit of a wake up call. We were training very hard at the time, ~15 hour track time (including warm ups) and ~15 hours weights per week.