Westie,
Several US Submariners have told me they would have surfaced the Boat and stayed on the surface to be able to ventilate the Boat as needed should the sea water generate toxic gases by mixing with the acid in the batteries.
They acknowledge it would have been a miserable ride home due to the sea state but the Boat should have handled it.
Do you have any technical explanation why that would be an unsound action to take considering the Boat's reporting taking on some water?