Roles aren't quite reversed, but they've come a long way. Dawson has evaded murder charges but is still dishonorably discharged; he realizes why—he was "supposed to fight for people who couldn't fight for themselves."
Kaffee, meantime, has apparently redeemed himself in Dawson's eyes. The two men can now salute one another in earnest, heartened by each other's honor. It's a great moment, pure Sorkin.