Smalma, I certainly don't have answers, only speculation.

I don't think genetics is the only or even the main mechanism where by hatchery fish damage wild fish. It looks like there is severely depressed survival for all smolts shortly after they hit the marine enviroment. In both cases, the Keogh (east side of Vancouver Island), and the Puget Sound stream you mention, there is not a release of hatchery fish in the particular stream, but there is a slug of hatchery smolts from nearby streams that will be mixed with the wild smolts as soon as they enter saltwater. It seems the regional depression of survival- both hatchery and wild smolts- is occurring in inside contained areas that are heavily loaded with hatchery fish. There is a good chance that in this artificial situation density dependent mechanisms caused by the hatchery loading are reponsible for the unexplained terrible returns. Mechanisms could be competition for food, attraction of predators that eat both hatchery and wild fish, behavior effects of hatchery fish on wild fish or disease amplification to name a few.

The Keough example you mention; isn't this the river that has been "fixed" by habitat improvement projects, large scale stream fertilization, and now a new hatchery program that is need to keep the run from going extinct. It seems this was a nice river that has been over-fixed to the point it is totally fouled up. I don't think you can make any inference of what is occurring based on this stream given all the different factors that might be responsible.