You can paddle your ship. That is the first thing that happens when yo hit the raise sails button and in the long ship paddling is slower than minimum wind speed for half sails and ~ 1/2 speed of maximum wind half sails and a little more than half speed for minimum wind at full sail and about 1/3 speed of full sails at maximum wind speed. The wind is definitely not purposely programmed against you and if it were you could easily game it by setting sail in the opposite direction from that you wish to travel and then paddling 180 degrees into what would then be fair winds. If the wind happens to be against you when you set sail use the sailing technique called tacking.

When tacking your long ship is always faster than paddling. With the Karve it is always faster than paddling at wind speeds higher than 2. With the raft its always faster than paddling at wind speed higher than 1.