I take your point but think that, in this instance, the injury to the man and the hypothermia of the woman caused the USCG to insist that they be taken off the boat. That the helicopter was nearing the extreme end of its range and fuel supply made that decision imperative without time to make any further consideration. Ankle deep water in the cabin is not a real threat to either crew or the boat. The report seems to indicate that the major damage was due to storm wave action and not water that entered the boat through the hatch. For sure, hatches should always be closed in heavy weather though. If the crew were not so incapacitated, they could have more than likely survived and brought the boat home without assistance. Four bilge pumps were certainly enough to deal with the water but, since they were not adequately shielded from debris, they all blocked.
Thinking about the rescues that have taken place off our local coast here around Cape Hatteras, I think these folk were much better prepared than most of them. A very high number of boats from which crew in distress is taken off continue to remain afloat long after the incident is over.