S7700, the reformed MAA and MilAAIB will be no sinecures, those who man them will be fighting two deadly opponents, aviation accidents and the MOD, and from day one. It won't be easy, but they will be carrying out their appointed duty in doing so. When they find operator shortcomings they must ensure that corrective action is taken promptly in order to avoid avoidable accidents. To do that they must have powers to enforce such action. That is where it gets really difficult. These are unchartered waters I admit, and nothing less than a complete revelation of all the evidence of illegal orders and actions, of subverting and suborning the mandated regulations, and so wilfully ignored by all the institutions charged with enforcing the law and punishing transgressors, will suffice. Aviation does not tolerate fudge, is indifferent to solemn and biding undertakings, it only respects 24hr continuous professional input to tame its suicidal tendencies.
I take your point that you and LJ make, that as publicly funded bodies they will be subject to Government interference from time to time. As I say, this will be no sinecure, and success in carrying out their mission will depend on the character and steadfastness of their leaders. Why would they want such a thankless task? Because I am convinced there are those who truly believe in ensuring Air Safety, not for bling, not for sinecure jobs in industry, but for the professional satisfaction of spending a worthwhile lifetime saving lives. Such people exist, such people post here, all they need is the opportunity to do what they know, what they believe in.
I am no starry eyed idealist. Life is never black or white, but many shades of grey (can't quite remember just how many for the moment). The CAA and AAIB have both had days they'd prefer to forget I'm sure, and the same will be true of the MAA and MilAAIB, but at least they can try to effect what they are now utterly unable to do, that is to carry out their responsibilities without constant meddling from the MOD's little helpers. There is a mountain of dross to be cleared up, making Stygian Stable duty appear to be a doddle. A lot of compromises will be needed to avoid grounding the entire UK Military Airfleet, but at least it will be recognised, assessed, and acknowledged. None of that happens now; there were no illegal orders, no subverting of the Regs, no substituting dedicated professional engineers with young ignorant non-engineers, no junior scapegoats (some of who died in the Grossly Unairworthy Aircraft they were manning), nothing to see here, we've all got homes to go to.
I'm surprised you put your faith in whistle blowers while acknowledging that the very people they inform either take no action or alternatively when they do, it's often not against the perpetrator but against the informer. As tuc tells us, it is official MOD policy that issuing an order to suborn the Regs is not an offence, while refusing to obey it is! Only an official body can hope to tackle such corrupt attitudes, individuals will simply be crushed.
LFH, I only excepted the Coroners Service because some of its Coroners have stood up for families and justice (though others have not). That you have issues with that generalisation I fully accept. I just take heart from anyone willing to do the right thing. It is my belief that when an example is set of doing the right thing, others are encouraged to do the same. We need to have faith in such people and remind ourselves of what is right and what is wrong.