PAG
To answer a few of your questions.... and I don't have an ATPL or a PPL but I do have well over 5000 hours. Does that count?
Yes "these civvies" are insured. Any civilian flying on a military aircraft has to be authorised, usually by the Stn Cdr, Group or Command, and is therefore on "duty" and therefore insured.
There is no cost to the tax payer. These sorties need to be flown for currency, currency that still continues after you PVR and before you exit the Service. All that happens is that a crew/pilot currency requirement is flown on a planned sortie that just happens to have a CAA IRE as a passenger. He observes what the pilots do and decides whether they have met the requirement for a civilian IRT.
As a reasonable argument I would simply counter with "why shouldn't it be done?". I know (please excuse the term) blunties who have got civilian qualifications as part of their career development within the RAF. Accountancy exams? ECDL perhaps? MAs? MBAs? Lots of these are paid for by the Military, and lots of people leave just after getting them. Resettlement is available to all and quite rightly so - but it can only be based around your current military qualifications. Remember the fuss not long ago about an SACW (IIRC) deciding she wanted to use her resettlement doing a pole dancing course? The "red top" papers made a huge fuss and the MOD said it was her choice to use her resettlement getting training in her new chosen career. End of story.
Obviously you cannot use an RAF aircraft to get more qualifications - for a number of reasons!! Firstly you are not RAF aircrew. Secondly you are not qualified on any military type. Therefore you cannot use a military aircraft to improve your flying qualifications. And sadly for you having a PPL does not make you more qualified - having 5000+ military hours means that I have quite a few exemptions towards an ATPL and an awful lot more (flying) experience. Likewise you should have more experience than I in your chosen profession.
This is a non-story and you do yourself and your colleagues a huge disservice by trying to make something of it. Hopefully you will see no "Me, me, me" in my reply and no need to "grow up" either. Unfortunately I think that you might need to!!