My views on these issues are well known on this forum by now. I fully support such safety programs as ASAP and FOQA, which are about trend analysis, not pursuing individual crews.
However, any agreement between management and the pilots' association must include a process by which serious and intentional incidents and deviations from SOPs can be dealt with. In short, the association must buy into all aspects of the safety program if it is to succeed.
The agreement must include a process that can identify and assist the airline when a serious, individual incident requires further enquiry. Sometimes that circumstance unfolds well because the crew itself, self-reports and is held harmless in favour of continuing the broader goals of the safety program - almost always, these circumstances and the individuals are known by most and management deals with the issue quietly and internally to the benefit of all. If you don't know or believe that, your finger's not on the pulse.
Again however, if we have intentional, serious deviations from SOPs, a good FOQA or ASAP agreement will have incorporated procedures and processes by which an individual pilot may be approached and his/her circumstances handled so as to mitigate then reverse any untoward operational issues. For some FOQA Programs, it's a "2 strikes" approach - if a captain is found to have two serious operational issues within a six month period, for example, that captain is interviewed and the reasons determined. Sometimes its the usual stuff like economic, personal or medical circumstances - Rarely is it a true "rogue".
The agreement with management then provides that such pilot is removed from the roster and provided with training, or medical assistance or whatever is needed to return that pilot, in healthy state, to the line. It is the pilots' association which takes responsibility for the crew member and who advises the airline that so-and-so member will be "off the line" for the "next two weeks - do not call".
That kind of agreement works. It is in place at a major carrier.
That is indeed, what true flight safety and pilot assistance programs are about when and if circumstances get that far.
That these programs have fallen apart speaks to both management and association failure to place flight safety ahead of other, less important issues. That those issues have not yet been elucidated speaks, I think, to the nature of the disagreement.
Believe me, I do understand how such issues can unfold. An airline trying to do due diligence and ensure that it is operating in accordance with FAA requirements but also trying to be fair to pilots who may be caught in circumstances involving all parties, is in a difficult spot these days when money, politics, and public impressions especially after recent issues regarding the FAA, are all impinging upon how management and the pilots association respond to these naturally-intrusive safety programs.