I think we can let the transients take care of it. I guess the problem from the residents' perspective is that the seal populations were able to grow about 10% a year once they were protected, and killer whale populations only grow about 3% a year, so the seal populations exploded and the transients are slowly catching up.
The nature of transient behaviour is to look for concentrations of pinnipeds, so if the pinnipeds are trying to take advantage of fish coming out of a river mouth, that'll draw transients, which will disperse the seals and eliminate the problem.
Seals are also important for vertical nutrient cycling; they'll take nutrients in depth and bring them up to the surface where they can go back into primary productivity.