Walaikum Salam Ma`am!
I am really very sorry about all that has happened. There are candidates who are fit, intelligent and fall into the ideal category for armed forces, yet even they somehow fail tests or get NOT RECOMMENDED.
Nonetheless, the medical fitness counts. There is initial medical examination at selection centres and then when a candidate is RECOMMENDED by ISSB, he or she undergoes a detailed medical examination. For Army, it is the nearest CMH to the candidate, whereas in PAF, the candidate is sent to CMB (Central Medical Board) where they check minutely.
Your son has only been disqualified by the doctor at selection centre. So it is unclear to you whether it is a permanent disqualification or a temporary. Keeping in view the case at hand, the permanent disqualification is handed over by CMB/CMH, means at later stages. Still, candidates can challenge the CMB/CMH medical examination through Appeal Medical Board.
I have no idea if you can approach Recruitment Directorate to arrange an Appeal Medical Board where the case is re-looked at to confirm the examination/conclusions.