Glen, under the Civil Aviation Act and the subsequent legislation, officer delegations and legal framework, CASA inspectors are permitted to evaluate regulatory risk, monitor compliance and then respond to non-compliance. In their mind they have done exactly this in relation to your specific case. To an observer or industry participant, what they have done is bastardise your company and sweep it out of existence for reasons only known to them. Absolute pricks. However, from a legal perspective they have shown that they have acted honestly and with due diligence by eliminating what they perceive as being a safety risk - you/your organisation. They will simply keep on promulgating that message, that they have acted prudently to mitigate and reduce a big scary safety risk to the dear Australian population. They will continue to present it in such a way that it is hard to dispute.
Winning against CASA is like chalking up a win against the Attorney Generals office or the ATO. It does happen, but rarely, and at great cost. Your hope should be that they view you as a pest, a thorn in their side (and successive and future Ministers sides) disrupting their busy Canberra schedule of coffee shop meetings and afternoon truffles, and hopefully they will offer you a few breadcrumbs to go away and leave them alone. As always Comrade, best of luck and we wish you every success.