Stan I agree with your idea re written direction, it was asked for, both in the case of unsafe practice, and in directions to alter certificated AFM procedures. My legal advice was that this placed the certification of the aircraft in jeopardy which in turn could negate the aircrafts insurance.
In all cases written direction was denied, however the inference was if you didnt do as you were told you wouldnt be permitted to operate the aircraft, so again damned if you do and damned if you dont.
I imagine the airlines have a robust legal team to challenge these things but what chance a GA operator affording that? and of course if you dissent even on safety grounds you are "Not a fit and proper person", so your in a lose lose situation.
I seriously believe now that it is CASA's policy to shut down GA. Why I have no idea, but at least they could be open and honest about it.