Jay,
Based on the information provided I have to guess there were multiple dislocations of your son's shoulder for DoDMERB to disqualify him. They should not disqualify for a single dislocation corrected w/surgery, unless your son still has some limitation of motion, chronic pain, or nerve damage.
You have 2 option. Once is to request a rebuttal of the disqualification, basically telling DoDMERB that they made an error and that your son should not be disqualified. If he has any of the items I mentioned above, DoDMERB will not remove the disqualification.
Second is to go for the waiver. In the disqualification letter that is sent by DoDMERB, it explains which academies and ROTC programs require a wavier request by the applicant. Regardless of which academy or ROTC program I would have your son write a letter to DoDMERB requesting that they forward it to the wavier authorities. In this letter I would have him state in his words what happened, what medical and physical therapy he has gone through as well as where he is at now from a physical standpoint, and what activities he currently participates in and how his shoulder bothers him, if at all.
If your son has not received the letter from DoDMERB the information is on the DoDMERB web site.