Nathan Drake said:
He then takes a 50% pay cut for some stupid reason.
Just because you don't know how the japanese companies work doesn't mean everything that happens there happens "for some stupid reason".
Any american or european company would have gone wild, blamed it on one single person and then fired that one single person regardless of whether or not he had anything to do with what went wrong. That person gets scapegoated, loses his job and is completely screwed.
The japanese company decides to put a reasonable pay cut (50% for iwata, 30% for the rest of the team) on all of the people responsible to make up for what went wrong. The people who had their pay cut will probably still have enough to pay their bills. They will have to live without some of their luxuries but at least their lives aren't completely destroyed.