didn't want to read and run. Just a quickie to welcome you first of all. Think first of all, well done on having an understanding GP. That's half the battle.
My daughter has been told not so swim at the moment. Her kneecap is tracking up the way (patella alta) and will probably need surgery. I don't think it's the swimming they are so concerned about but the getting out of the pool, easy to just jump in, but getting out is another matter
I think the biggest thing is only to do exercise that you're comfortable with. The only thing my daughter is allowed to do at the moment is a minute on the exercise bike to build her quads for if/when the surgery is required. You could also ask for a second opinion, and ask the physio for some core strengthening exercises. It might also be better waiting to see what the results of the MRI are.
Have a good old read on the forums, you'll find some good advice, like sleeping with a pillow between your knees if they are slipping when you are sleeping, I keep repeating that one because it's helped my daughter and even me with my arthritic knees