The knee was designed so that you can walk, run, squat down and pick things up. If you can’t squat then something is definitely wrong. If you damaged a part of your knee then more than likely you damaged your ability to walk, run, and squat down and pick things up.
To rebuild your knee you need to work it back to being able to do those things if it is possible. With your damage I believe it is possible, the only problem is now it is a very sensative process. You need to apply enough stress to adapt the muscles and tendons, but not to fast as to stop the healing process. There are a billion conflicting articles on what not to do with the knee, what this tells me is no one has mastered it
To Sum it up being able to squat is natural and healthy and ok for your knee when done properly.
High protein says nothing by itself. If you eat alot, you eat high protein carb and fat. If you are talking about things like atkins diets, simplified versions of these diets are bad for you. I’ve seen people who read parts of these diets then go out eat steak every morning noon and night. This is unhealthy. Please notice that these are High protein diets. Not eat only protein diets.
There is a ton of information out there, unfortunately people tend to read the first paragraph, when taken in parts this information can be very very harmful.