2nd Gen
You are not alone in this type of situation - especilly amongst new CPLs. All I can offer is advice on how I deal would deal with this dilemma.
You fortunately have the advantage that the issues in question have maybe not led to an accident already.
Consider this.
Place yourself in a situation 3 years from now, way after you had left that company and moved onto bigger and hopefully more professional things. You read on PPrune about an incident where a pilot at the company you used to work for had been tragically killed and that one of the contributary factors may have been one of the issues that you are presently in a quandry about eg fatigue.
Would you feel guilt that, had you supported you friend and spoken up at the time is it possible that this tragedy may not have happenned?
If your answer is yes - I would feel guilty, then you must speak up.
Within the Senate Inquiry we are asking industry to ignore their own interests, commercial or otherwise. As pilots we must do the same regardless of personal consequences if we are to achieve the common goal of improving safety within the Australian aviation industry.
Good Luck in making your decision.
The Kelpie