I didnt say it was an easy solution. I am also not sure that deadly force is always called for. If a camper wanders into a forest the company doesn't shoot him unless he is trying to steal their trees.
The military situation below is similar. The submarine is not in the water to fish.
Clearly agreements would have to be made and enforced. But, we have managed to do so on land and air, I see no reason why it would not be possible with oceans and GPS.
"The military situation below is similar. The submarine is not in the water to fish."
Let's assume its presence is damaging the fishery. (Scaring away the fish, etc.) For example, a "hiker" engaged in tree-spiking can (and has) been shot by security.
OK, so Country B has just lost a submarine to a corporation chartered in Country A.
What next?