I have two responses to the additional comments.
First, if it is true that under NZ law the company's procedures take on the affect of law once they are approved by the CAA then by definition there is a conflict in the law. The law governing when ATC can give permission to take off and the law governing when a pilot had legal authority to take off are in direct conflict with one another. Therefore, it is the law which is unsafe, not the pilots behavior. You solve the conflict in the law by changing it; not by charging one party and not the other.
Second, if it is true that under NZ law the company's procedures take on the affect of law once they are approved by the CAA then by definition the company is a guilty as a pilot. There is nothing in the law as quoted on these forums that exempt the company from being found criminally liable. Who employed the pilot? The airline. Who supervised the pilot? The airline. Who is responsible for the pilots behavior. The airline. The pilot has no independent authority to order a take-off of the airline's airplanes outside of the scope of his employment with that airline. If he is guilty so must they be.
The more information that is posted in this thread the more obvious becomes that this is a hatchet job. The pilot pissed somebody in authority off somewhere in his/her career and that person now has found an excuse to screw him over.
A shameful case for NZ as a country.