I've had dodgy knees for two years, and I can't even walk or down the stairs. All I can say is that the leg press and extension have been MORE painful for me than bodyweight squats have been.
Granted, my problem isn't exactly the same (I have cartlidge issues in one knee + hoffa's fat pad syndrome) and also tendinopathy in the other. Has she tried static holds in certain positions that aren't so painful?
I'm sorry I can't be too helpful - after all, I've failed to sort my knees out for the last two years.
Btw, is it impact that hurts more or is it putting the leg through a certain angle of motion that hurts?