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Running shouldn’t hurt or harm your knees, in fact it’s more likely to be beneficial.

You might find stability shoes to be beneficial until you’ve built up the right muscles, high stack shoes can be quite unstable.

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Of course it is beneficial in the long run, but beginners are still prone to overtraining and getting injured when they go from sitting a desk for 14 hours a day to running 3 times a week

Your knees should never hurt, overtraining or not.

I wouldn’t say “never”. Stuff like ITBS presents as knee pain when the actual problem area is typically weakness in the hip, for example.

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