Great post Giff and congrats to you and your son for his commitment to Pepperdine. Typically, I'm of the mind set that potential recruits can and should do this on their own given enough time and planning. I don't know your exact situation but it seems like your son was running out of time and you decided to do something about it. Fair enough. Many of us may have done the same.
Every personal conversation about recruiting I've had on this website has examples of RCs or HCs passing on a recruit who would be a perfect fit at their school. It always comes up. I look at it this way....you did everything you possibly could do to put him in a winning position with the Naval Academy. Based on everything you've shared, he would have been ideal for Navy. Bottom line is your son only gets one chance at this (freshman) recruiting thing and it didn't work out. You'll never know why, and that is the part that eats away at people. Something similar happened to my son. He had the added benefit of playing against a certain team (that passed on him) every year in conference. He loved pitching against them! Once your son is on-campus and fighting for playing time, all of this "why didn't they recruit me" will go away. He'll have bigger fish to fry, and he'll realize this is where he belongs.
JMO and Good luck!