I think that a waiver may be required if the injury is fairly recent and the doctor hasn't given the all clear. IIRC, that usually comes 6-months to a year after the surgery.
In my daughter's case, it was handled through a remedial after her DoDMERB physical and questionnaire for AROTC. We provided complete medical records (hers was a red-white medial lateral tear). Her's was between 8th and 9th grade, followed by 4 years of 3 varsity sports. From my exchanges with Mr. Mullen back in the day, it never entered my mind that it would be an issue.
YMMV