Even if this had been a vertical scroller, the boat can still turn, and you have the same issue. There are other solutions, like having the keys map to absolute direction, but that loses a lot of the flavor of controlling a ship (turning, trying to keep enemies abeam, etc.). Alternatively you could have the camera attached and rotating with the ship, but then it wouldn't be a scrolling shooter.
The only other good option I can think of would have the vertical axis control the set of the sail (Furling/Unfurling) and the horizontal axis the wheel, but we didn't have time to get to this.
Thanks for playing!