In my view, it shouldn't be left to 22(Trg) Gp to manage this; it should be the MAA because it's very much an airworthiness issue. Perhaps the CAA and MAA are already working together on it?
It is not really a CAA decision - CAA will shortly just become an executive national arm of EASA, and will not be responsible for formulating the regulations. The MOD would probably need to negotiate directly with EASA.
If the MOD really think it important to maintain parallel civilian qualifications for aircrew, why not apply for EASA FTO status?
The EFT course is already staffed largely by civilian qualified instructors, so presumably is already not far from meeting FTO requirements.
Presumably 45Sqn already train and test to at least the standard for award of a CPL and SPA IR/ME? They would need to parallel qualify their QFIs with civilian qualifications, but this would be a CAA (rather than EASA) decision since national authorities are still responsible for issuing instructional qualifications.
The advantage of such an approach is that the MOD would be able to obtain all the relevant authorisations from the CAA, rather than expecting the CAA to go cap in hand to EASA to negotiate an exemption for the MOD.
The French Air Force anticipated this when EASA was formulated and have for the last ten years or so put all their pilots through full ATPL theory immediately after flying grading with the intention that those who stream to ME can get parallel civilian qualifications, and those that fail EFT or get streamed to FJs at least have some useful qualifications to full back on. I understand they are now indeed working on FTO status for some of their training establishments.