What can I do about my sore knees? My GP thinks my high impact workouts are to blame? I love the gym but worry?

There is an old saying "whatever you do, do in moderation", you are clearly working at a punishing rate, I am rather surprised that your trainer is allowing this! Slow down, it is not a race, twice a week is enough, believe me, if you destroy your knees now, you will live a lifetime to regret it! Good luck.