This is what is known as "the double bind problem" and it is endemic to Australian commercial aviation as far as I can tell.
1. You are required by law to comply with safety regulations under threat of prosecution.
2. The corporate culture punishes anyone who raises a safety sensitive matter with any regulator.
The pilot is in the middle between a rock and a hard place.
Report something and you are moral, legal, but have no career.
Don't report, and you will have a career, but will carry the judicial and moral liability for your employers failings.
Exxon and BP are masters of this strategy.