Although we haven't had a chance to read the book yet, the impression I'm getting is that Kerry's comrades basically said "give him the damn purple hearts and get him the HELL out of here..." Whatever it takes.
One thing that's overlooked is that Kerry's father was some sort of a "diplomat," as told to us in the Spielberg convention bio film... could it be that JFKerry was considered a VIP and that the chain of command didn't want to mess with a VIP and all the attendant political issues? In other words, maybe it was easier to give the brat what he wanted and send him home, because he was dangerous!
Probably more significant is his association with the Kennedys. I don't know that his father was all that high up as a diplomat. The Kennedys, on the other hand, were royalty.