POBJOY, point taken re the CAA, and indeed EASA, Clive Watson! I don't pretend to offer a blueprint for sorting out the scandal that is UK Military Airworthiness, but others created a system that assured it in the past. The trick is to do the same, but this time to ensure its independence of the operator (aka the MOD) and the investigator (which must be made independent of both).
You speak of Mark 2 airliners, but their airworthiness was assured by that very arrangement in civilian aviation. Those engineers that were so engaged did so under the authority of an independent Regulator, just as the ones who assured the airworthiness of lesser technologies, such as gliders. Even the engineers who maintained and serviced these different types did so under the authority of the Regulator, rather than that of their employer. If that system that worked so well has been "mended" then I would question the efficacy of doing so. The military system though is well and truly bust and has to be mended! I still say that the civilian model of Operator, Regulator, and Investigator, all separated from, and independent of, each other is the way to go.
All that said it will take a great deal of time to return Military Airworthiness to a functional state. Anything worthwhile takes years to build and mere minutes to destroy. So it was with UK Military Airworthiness Provision and Maintenance. As I said before this will take real leadership to achieve. A new Trenchard is needed, someone whose name will be forever linked with this essential reform.
The very first requirement is to acknowledge the situation and to start that reform on its way. Perhaps the CAS, who has personal experience of the realities of conducting an investigation into a military aircraft accident when not independent of the operator, might be so minded...