You have GOT to be kidding!
Air Miles are a 'perk' awarded to the individual - and you are under no obligation to join any frequent flyer programme in order to use them. They cannot be transferred to anyone other than the person who travelled, in any case. So no, you cannot 'hand them in' - nor can anyone else use them on your behalf.
Join the relevant frequnet flyer programme personally, then send your boarding card in retrospectively and ask for the Miles to be credited to your account. No need to tell anyone.
Does the pathetic cash-strapped MoD have the slightest clue as to how many flights are needed before these 'Miles' are of any use for travel purposes?