The gov't doesn't care about the shellfish, they care about the livelihoods of those fishermen. If they were to switch a new ocean farming technology those fishermen would be out of jobs.
Plus, the beds can only be fished so hard at a time or they start to dry up, again leading to loss of jobs.
Really, for the otters to be that much of a problem, it has to be that the beds are small to being with. If the beds were really large, in order for the otters to matter, there would have to be hundreds of thousands of them.