PIC authority and responsibilities - not minor matters (or disputes)
The development of whistleblower protections in statutes and statutory terms is way, way beyond the scope of the thread - but I agree with and appreciate your post, peekay4. Clearly if the facts are as you have indicated, then the Capt's legal position indeed would have been squarely, I mean right down the middle of the strike zone, within the zone of interests sought to be protected by AIR21. So . . .
. . . I suppose a subject for discovery, particularly deposition, would be the captain's thought process about why he elected not to avail himself of those protections. Once again, conventional litigation in a court of law will prove to be a most inefficient means of getting at the underlying issues in the particular situation - yeah money and intangibles will be bought, sold and paid for, but the larger interests invoked -- or called into view -- by the disputes will be mere litigation wallflowers. Too bad no one has figured out how to move the system toward "interest mediation" - resolution of the case or controversy, like ordinary mediation, but with policy or procedural reforms mandated by the outcome, akin to interest arbitration.
Back to the ABX litigation you mentioned earlier, for a second. . . that suit was brought by the collective bargaining representative of the pilots of that air carrier. Under the Railway Labor Act. Do you think the course of such lawsuits (as a specific example), and the generally antediluvian nature of cross-ties and steel rail technology as compared to today's complex approaches and the technological complexity of air carrier aviation overall (as a general point) signal that the time is upon the U.S. to move aviation labor law out of the steam engine era? (I am indeed aware of the puppy-tail-chasing machinations of the Congress on something as relatively straight-forward as FAA re-authorization, but, hey, it doesn't hurt to ask.)
Cheers! (and Keep Your Eyes on the Sky . . .)