It seems there are lots of questions here.
1) Can he pick up his luggage in FRA or IAD?
Yes, specifically IAD, as he'll actually be required to pick up his luggage there.
2) Will skipping his last flight be a problem?
If you skip a flight, all subsequent flights on that ticket will be cancelled. If you skip the last flight, you are therefore fine.
The problem is if you have a problem with any of the flightS, the airline will have no obligation to get you to DC, only Jacksonville. So you could get rerouted through New York or Chicago.
As for whether the military would have a problem with not flying all legs of a ticket it bought, I have no idea.
3) Where can he find a cheap flight?
This gets asked a lot here. But when you don't have flexibility on date, time, origin, and destination, there really aren't any secrets. Look at kayak.com or google flights or whatever.