From Moosp:
That Corporate Safety instigated the investigation in the first place is extremely worrying, and may affect the accuracy of the data that they receive over the next few years. By their actions on this incident they have shown perhaps that they are not the impartial safety team that they have always claimed to be. They have shown that they may have a political agenda.
Under the James Reason model of a "Just Safety Culture," the company should forgive unintentional errors that are disclosed freely in the interest of collecting data to prevent reccurences. However, it should not tolerate blatant and wilful violations of procedures and regulations, or cover ups. I don't see how the safety department's actions in this case runs counter to industry best practices. (I just hope they've given the Chairman a briefing on leading by example...!)
Aviation history is littered with crashes that could have been prevented by someone noticing someone's increased appetite for ego-stroking and risk taking. A few are discussed in this excellent book:
http://www.amazon.com/Flight-Discipl.../dp/0070343713