Disclaimer: I am not a medical professional. I'm not an MD, OD, DPT, RN etc. I am a CrossFit Level 1 Trainer with 7 years' experience coaching, with an expired Wilderness First Responder card. I cannot diagnose or treat.
Now that that's out of the way, what the hell is wrong with you? I'm talking to those aforementioned medical professionals who tell my athletes they shouldn't squat below parallel or worse, tell them they can never squat again. Then, you give them PT that loads the knees far worse.
We've shown time and time again that squatting to a point where your hamstrings take up some of the load through your knee is safe, healthy and a damn sight better than anything else. I'm not talking about the ass-to-ankles squat necessary for high level Olympic weightlifters, but the hip crease below the knee squat. CrossFit's been teaching it for 17 years with no ill effects. I've been teaching it for 7 with no ill effects (even the folks with knee issues seem to not have them when they squat properly).
The hazard comes when you get people afraid of a basic human movement. Granted, people with Osgood-Schlatter disease maybe shouldn't set powerlifting squat records, but they should be able to mount and dismount a toilet without flopping. Same goes for the elderly. If you have them avoid the movement, then the risk of them getting injured when they have to do the movement (like getting up off the floor or toilet) increases hundredfold.
For you, the concerned athlete, use your head. If your knee injury is acute (recent and result of a direct impact or obvious injury) maybe don't squat or lunge for a while. Get it checked out by a professional. Preferably one that does things that you like to do. They don't have to CrossFit, but maybe they like lifting or cycling or running. They'll be more understanding of your desire to get back to fighting shape. Be wary, just like you'd be wary of a dentist with messed up teeth or a cardiologist that weighs 400lbs and smells like cigarettes.
Most doctors and PTs don't lift or do CrossFit. Hell, even exercise sport "professionals" don't do them either and they sure as shit don't have hands-on experience teaching or observing correct movement. Ask anyone who's been in any of those programs how much time they spent teaching evaluating and correcting the squat. 20 minutes is the answer you'll get. Then they'll have you do PT that put inherently more torque, pressure and strain on the very joint they're trying to rehab. They'll tell you your glutes aren't firing properly, and have you do crossovers with bent knees. <insert yuck face here>
I won't ever push you into the pain zone. I'll never make recommendations that are not couched in experience, professional education or common sense. All I ask is that you maybe don't listen to just one medical professional, and if the one you have doesn't give you a good answer find another.
20 reverse lunges
15 EB good mornings
10 EB push press
Benchmark WOD "Diane"
Deadlift M:225 F:185