Ending--WTF?!

I think the point made at the end is the conduct of his officers led to that situation. And he is right.

Maryk was right. It doesn't matter that he wasn't a psychologist. He was an experienced naval officer, and the helmsman also seemed to be experienced. They both thought the ship was in danger of foundering and that something needed to be done, immediately. Queeg snapped. He couldn't handle the pressure, and he froze. If Maryk had not taken over and given the correct orders to maneuver the ship, it was highly likely the ship and many of the crew would have been lost.

Zen , I just saw the movie for the first time and had the exact same reaction to the ending as you. I'm glad to see your comment, in fact , because after seeing the movie i immediately searched the net to see if others had the same reaction as mine or whether i had missed something.
Greenwald's drunken rant against the defendants seems to be completely inconsistent with what was exposed in the courtroom thanks to Greenwald's aggressive questioning of Queeg. And even though Keefer might have been a cowardly, oily character, ultimately his assessment of Queeg as being paranoid was proven to be correct - even one of the court appointed psychiatrists admitted that under cross examination. To suggest that Queeg would have been ok with more support from his officers and less stress is a bit of a stretch The missing strawberries saga alone showed Queeg had serious issues. It was hardly a stressful situation, esp in a war environment, that he blew up into a major incident even after he was told what really happened to the strawberries by an eye witness. It showed Queeg was a bit of a nutter and therefore it was no surprise when he cracked up under a real stressful situation - the storm. And of course Maryk did the right thing by assuming command from Queeg then. in order to save the ship and the crew

Having said all that, the courtroom drama is excellently scripted and acted. The ending is intriguing, albeit a bit confusing, and very different from most movies I’ve seen, and every movie I’ve ever seen from that era. Rather than having a stereotypically happy ending with a simple resolution, it attempts, via Greenwald's rant, to paint most of the key players as various shades of grey rather than either just good or bad,with the darkest shade belonging to Keefer who Greenwald identifies as as the real villain and cause of the mutiny. Keefer is obviously not a very nice character, but is hardly evil. I also can't see that he's responsible for the mutiny which was was justified anyway..

They had the opportunity to deal with the matter in accordance with proper procedure including bringing it up directly with Admiral Halsey. The fact that they didn’t was negligence on their part.