Post a video of your squats. It's very likely that your form is the issue, not the knee injury.
As for that rehab protocol, start with the bar for high as hell reps, and add weight (10 pounds is a good starting point) to the bar every workout, tapering the reps down as the weight gets higher until you're back to 3x5.
Physios are generally clueless about training. Much has been written on this site about their silliness.