Hmmm... That will bring a new map style: make narrow water paths with rocks. After dealing with them, you can pass with a ship and fight/build something :)
I would not touch it before release 19, because it is quite sensitive and can lead to problems.
Also note that fleets are static, the code does not expect changes in waters, like interconnections of separated waters and vice versa. So as I said this is not so simple...
Maybe add a check to the pathfinder that the field mustn't contain any immovables that have a size > 0?