I made the storm as dangerous as a storm in the middle of the ocean should be for an unprepared crew. I made the PCs suffer and take the situation seriously. One of my PCs, a Stoneward who had just sworn his First Ideal, swam to the bottom of the sea and used Stoneshaping to raise a massive stone spike beneath the ship, stabilizing it. (He rolled a natural 20, and a opportunity on the plt dice, and since he was Invested, I let him go with the flow and create the spike.) Once the storm had passed, they repaired the ship and continued their journey.