Marina Hyde in the Guardian comments:
Career civil servants don't take unilateral policy decisions, let alone ones that might place their career in jeopardy and threaten their handsome pensions... The popular caricature of studied inertia in the upper ranks of the civil service is funny because it's true, as Homer Simpson would say. Every atom of the career civil servant's being is dedicated to avoiding personal risk.
From my interaction with civil servants I think this is true. One of the reasons I did not take the job which was offered to me in the Civil Service is because I find it stultifying, boring, and inefficient, precisely because of the obsessional risk-avoidance.
However, there is another feature of Civil Service life which I think is relevant. Senior people use their powers to push risk onto junior people. That is, the people who are paid least are forced to take most responsibility. A senior person will write an email which says something like 'Document turnaround times must be reduced by 2 days'. A reply might be 'We can't reduce turnaround without compromising validation procedures. Do you want to authorise a change in those?' and there will be no reply. This is just a made-up example, but you get my drift. Junior people are set objectives which require rules to be broken, and everyone knows that is what is being asked, but there is no explicit command to break rules.
I suspect that Brodie Clark has used this tactic a few times himself (I don't know). Now it has been used on him. I suspect that orders were undocumented, deniable, and possibly made by inference. If I am wrong and there is proof that she ordered it in explicit documented words, then she's acting crazy to deny it. It's possible she's that reckless, but surely not that stupid.*
On the bigger picture around this event: scapegoating senior civil servants to divert blame from Ministers is a clever short term tactic but a poor long term strategy. Well paid Mandarins are on the whole not good and selfless people. They are wily and amoral. If they see their colleagues being burned they will act to protect themselves.
*ETA It's possible she's unsackable (as this article argues). In a way that makes her behaviour even more reckless.