tkdgirl,
The waiver authorities for each service academy and ROTC program are separate, except for USNA and NROTC. One waiver authority can deny a waiver while the other will approve it, even for the same branch of service. So in your case there is a possibility that AFROTC could approve your waiver even though USAFA has denied it.
You can also request that USAFA re-look at your wavier package. Just write a letter to DoDMERB requesting the wavier authorities reconsider their decision.