If the master ultimately lost his job for his decision NOT to put to sea, then so be it -- that's called "moral courage" in the military, and it is one of the many factors that differentiate a "profession" from a "vocation."
I agree that in retrospect it seems overwhelming that the captain's decision to leave port was a bad decision. It's possible (though purely speculative) that he was influenced by pressure from the "main office" (perhaps driven by financial interests, especially given a possible desire to have the boat available for viewing by potential buyers in Florida).
However, I need to call you on the "armchair quarterback" aspect of your statement. It's real easy for any of us to sit back and call the captain a coward for not being willing to lose his job. Large organizations like the military and major airlines have organizational infrastructure in place to investigate and protect a captain/pilot's decision to scrub a trip due to safety concerns. One of the things I take away from this whole incident is the comfort of knowing that when I get on a commercial aircraft, the pilot has a powerful union to back him up if he scrubs a flight for safety reasons. I'm not the world's most pro-union guy, but I can see that a union serves a useful purpose in this situation.
Contrast that with a captain working for a small, financially struggling foundation. If he lacks the protection of a union (a bold assumption on my part), all of a sudden the pressure on him may be much greater.
Any good investigation has to look at the culture of the employer. When I say that undisclosed facts can greatly change the interpretation of events, this is part of what I mean. It's possible that the root cause was not the captain's choice to go out in THIS hurricane, but was the decision to go out in his first hurricane ~15 years ago.
When it comes to safety, there is often a tendency to fall into creeping incrementalism, where cutting a corner and getting away with it one time leads to cutting even bigger corners later. Like launching a space shuttle at ever-lower temperatures, and ultimately below the glass transition of the rubber O-ring (think Challenger disaster), or growing complacent over the repeated impacts of hydrogen tank insulation on the ceramic front edge of a wing (Columbia disaster).
In these cases, the root cause was not necessarily a decision made on the day of the launch, but rather resulted from a gradual erosion in the overall quality of judgement starting months or years prior to the actual accident.
So the lack of "moral courage" that you were referring to may not have happened in October 2012, but in earlier decisions that the captain made. It's possible that he should have sacrificed his job 10 or 15 years earlier because of his initial poor decisions to go out in prior hurricanes. But if those earlier hurricanes had changed course and made this captain look like a coward for not going out, how many of those guys on gcaptain would have been defending him? I suspect they would have been stepping up to take his job after he got fired.
The USCG has a lot of expertise in this area, and I expect that their investigation will reach back well before the day the captain decided to go out into the hurricane.