Similar issue for me, I played soccer for about 17 years and ran track for another 6, so I was conditioned to pursue cardio/aerobic/running based exercises. I started having shooting pains in my knees at 22, which I have since learned is due to a loss of cartilage and fluid in my knees; the doctors estimate I'll need one or both knees replaced by 50. I also have chronic lower back aches that the chiropractor tells me were caused by the millions of footsteps and kick-plants I did over all those years, which now causes me to carry about 30 lbs. more on my right foot than my left. So I definitely can attest that high-impact cardio/aerobic workouts can do long term damage.
Unfortunately low-impact aerobic workouts tend to require a machine of some sort (elliptical, rowing machine, etc.) which would force me to actually go to a gym. I was too lazy to do that before I had a kid, let alone now. Fortunately I still have a pretty high metabolism so I'm only 20-30 lbs. overweight, but I'll be happy to hear suggestions on stuff that can be done at home.