The MoD have signed up to this. Under the Transport Act 2000, the Secretary of State cedes power to the CAA to ensure the safe provision of air navigation services; the MoD have agreed to broadly comply with the Act unless it is a matter of direct national security.
(see this link:
http://www.caa.co.uk/docs/7/DirectionstoCAA.pdf )
Consequently, CAA (DAP) is a joint and integrated civil/military organisation which formulates and implements common policy regarding the utilisation of airspace.
Call the number - I guarantee you will get an honest answer. (Don't call tommorrow because the individuals you need to speak to will be out of the office).