Leaving the boat and putting the bears on the island was the most dangerous way forward, and everyone knew it. They were leaving themselves wide open to attack. The captain made his decision.
They were just going to have to be brave, and do it. There was no other way to ensure the cubs would be safe. They took the cubs to an area of woodland on the island, and they set them loose. All the time, they were nervously glancing back over their shoulders.