Whether or not the correct legal processes have been followed is largely irrelevant in term of the moral position.
So, the Treasury Solicitor was not served with the papers. And a lengthy redress procedure, which may or may not have found in favour of HA after many months or even years, was not gone through. All this means is that MOD will get off on a technicality. There can be absolutely no doubt here in my mind, that the MOD are morally liable for this state of affairs getting as far as it did. I would possibly even go so far as to say that which ever senior officers signed off on the whole JPA debacle are guilty of negligence - it should have been clear to almost any reasonable person that implimenting this system in the way they did was bound to be a disaster, leading to problems of under/over payment and general administrative failure.
If nothing else, I hope the publicity surrounding this case has embarrassed a few of their airships into looking into just why JPA is so unfit for purpose and doing something about it.