Long-distance running is a natural human activity and is not inherintly bad for your knees
I can't find a decent journal article, but the general consensus is that running is not bad for your knees. It is theorised that endurance hunting (i.e running after an animal until it dies of exhaustion) was the first form of hunting of humans.
Bad shoes lead to bad knees, lead to worse shoes, etc...
There is big difference between how we ran in the distant past, and how we run now. The rise in knee injuries happened shortly after the "westernisation" and commercialisation of long-distance events such as the marathon. During the fitness crazes of the 1970's and 80's more and more untrained adults began to do fun-runs and marathons.
However, because they were unused to running they would run with a heavy heel strike causing high pressure and damage to the leg joints. This lead to the evolution of the modern 'running shoe'. This in turn lead to heavier heel strikes, and the sudden pressure their of increasing hip, knee and ankle strain. Eventually shoes then looked at eliminating ankle roll and pronation to reduce ankle damage, again leading to mroe damage. The reason for this was there was little sensory feedback from the foot and muscles to know what it was doing was unsafe until it was too late.
Decrease your risk of damage by using a minimalist shoe.
To prevent the risk of long term joint damage you may want to consider minimalist shoes. Its only recently that the modern 'minimalist' shoe has evolved, that paradoxically is safer. By forcing the entirety of the leg to actively cushion the foot fall, this leads to a safer, softer mid-foot strike. If you are looking at distance running regardless of shoe type, begin slowly, in terms of both pace and distance, and train on how to perform a good mid foot strike.
There is a lot of emerging evidence that suggests that the musclar adapatations for running minimalist shoes will provide support and protection for the joints, while encouraging a safer running gait that minimises the force driven into the ground. If you heed this science and your own body, your risks of knee damage from running will likely be no more than the risk of anyone else.