Out of fairness to said officer, the practice of destroying embarrassing evidence long pre-dates his tenure. The RAF tried it on Mull of Kintyre once the campaign really kicked off in about 2000 (the FoI Act being a major factor) but forgot that MoD(PE) had control of most of airworthiness audit trail prior to April 1999; and those with delegation were told to keep copies of everything they signed, even into retirement. (This doesn't sit well with the Official Secrets Act, but show me a prosecution. MoD won't go there. And Des Browne granted immunity). So, when the Air Staffs and their bagmen denied the very existence of these documents, both to Lord Philip and the media, the former was delighted to receive copies from former PE staff. And quickly took to asking them first, not MoD. Even then, MoD continued to deny their existence, lying to bereaved families. That is not one lowly Gp Capt. That is a directive from God, and (e.g.) DE&S's Secretariat is charged with protecting those who lie - knowing he is protected.
Rest assured, there is sufficient evidence of wrongdoing. First and foremost, CAS's admission that there was no safety case, so by definition a series of ACASs made false record. This is nothing new - Chinook, Hercules, Nimrod, Sea King, Hawk - the list is only constrained by the aircraft types we have. It is therefore unfair to blame one person; but that is MoD's wont, witness the character assassination of Gp Capt Baber in the Nimrod Review. In fact, he deserved some praise for letting a safety case task, as he'd inherited the product of a policy not to waste money on such things.
One view I take in all this is that ACAS became the first DG/MAA in 2010. He would have immediately released (if not told already by Haddon-Cave) that most of the RTSs (the Master Airworthiness Reference) he signed were invalid. Including gliders. Why did it take four more years, and require his successor to step in? There may be a very good reason, but demonstrably the failures persisted in that period, and more people died. I'm afraid we see this too often. Bury the bad news until the perpetrator is retired, then spin the problem as something else entirely and blame a junior officer or civilian. Yes, the Gp Capt took part, but he's a very minor player.