Yes, providing the tube that the rudder shaft goes through is undamaged - and the top is above the water line - it should be possible to remove the rudder with the boat still in the water. I did it with my cat, after snapping one of my rudders in half (photo).
I found that the biggest problem was the buoyancy of the rudder making it difficult to pull it down. I solved the problem by tying rope around the rudder so I had something to tug on. Having a hookah was helpful too.