Treasury, not MoD
The future of Northolt is not in the hands of the MoD at all. HM Treasury will decide its future. You don't think that lhr runway 3 got passed by the strength of the DfT?? It was HMT, not DfT that argued for it on Economic grounds.
If the CAA say that NATS cannot produce safe airways from R3, then HMT will decide to close Northolt on Economic grounds. End of. They'll sell it off for housing.
RAF can then go to Wycombe or further west - it has no current Mission based need for Northolt.
A bit like lhr, it is there by historic accident.