I'll avoid taking a position on the merit of the 'two on the flight deck' argument, but the unintended consequences would have been obvious to anyone at the time the rule was implemented.... unless of course the rule was merely implemented as an overnight knee jerk reaction to an reasonably isolated incident.
Regardless if whether there is merit for the two on deck policy or not, it strikes me as very weak of CASA to handball the problem to individual operators rather than take a stance themselves as the regulator.