If the Chief Pilot is leaving surely this should start to indicate to CASA there are issues internally, when you have seen strong growth with the business growing from 20 aircraft to 28 and staff number increasing from 550 to 750 and with multiple key persons walking out then then from a CASA perspective this would be sending their AOC risk profile score on the upwards!
CASA wouldn't have the intestinal fortitude to take a stand like that against Qantas or any major airline for that matter.