There is no doubt in my mind that the two pilots will eventually be cleared. And now it is out of the hands of the MoD how it is done. If the mandarins and retired officers had thought about it, the better option and least damaging to themselves and the MoD would have been to have cleared the pilots of negligence before the minute details of the acute lack of airworthiness became a matter of public consumption.
Now, however, it is a completely different story, I rather suspect the outrageously negligent implementation of airworthiness regulations will be central to the unfolding story.
I expect, that once again people will be named and shamed. After the Nimrod tragedy many were quietly "retired", moved along etc. Surely time has come for those responsible to appear before a separate court and answer for their actions. The MoD appears to be beyond learning the most important lessons.