Is there an appeal process for the Waiver rejection? One would think that given a Marine clearance the Army might reconsider.
It sounds like USNA was seriously considered and only rejected when he was forced to choose by the MOC. I would suggest, assuming there is no waiver reversal by the USMA, that your son attend a civilian college, participate in NROTC, and then get nominations from both the NROTC Commander, and the MOC. Given the USMA LOE, it is likely your son would be accepted into the USNA next year.
I'm not sure exactly how the USMA curriculum is "broader" than that at the USNA, other than a greater % of non-technical classes. On the other hand, many would conclude that the USNA offers a broader spectrum of active duty assignments... fixed wing NAVY, rotary wing Navy, fixed wing Marine, rotary wing Marine, Marine Ground, sub-surface ships, surface ships, Nuclear powered vessels, and the various army-like assignments in Marines other than Infantry.