I think they're Civil Service. At one point remember, Kate asked Tony if he was a GS9 or a GS11 (or something - I don't recall the numbers). That means they've got the same rules as every other GS employee.

It *could* be that he *does* have plans for Tony, but needed him to have that experience or to have made connections with certain people in the Seahawk's crew.

Time will tell. :-)