As Robert indicated, the SF was recovering nicely following the St. Helens blast. The 80s were good recovery years as there were no major floods, and marine survival rates were good for steelhead. The 90s were almost the opposite. Floods in 90 and 96 especially, and the low marine survival during that time period combined to set the clock back for SF steelhead to about where it was right after the blast. The 96 flood destablized and released a lot of the blast sediment that had begin to stablize. The improved ocean survival of the last couple years should benefit any wild fish that persisted following the 96 flood. As the blast sediment settles toward stabilization again, the steelhead run should rebound. This cycle of improvement and setbacks for the SF watershed will probably continue for a few decades, as the watershed was really hammered by the blast: witness the NF, which will probably take a lifetime or more to recover.
Stocking summer run steelhead, in and of itself, is highly unlikely to be the proximate cause of the depressed condition of the native winter runs. It is possible, but in order for that to be the case, the following would have to occur: the hatchery smolts would have to almost all be severely under-sized at the time of their release, causing a very high rate of residulism in the SF. The residuals, being larger than yearling wild steelhead (most steelhead smolt at age 2), would then compete for food and space with native juvenile steelhead. There are always some residuals from hatchery plants, but I've not heard of anything excessive regarding the SF. It is important to consider that there are many fairly healthy wild native winter run populations that share rivers with hatchery summer runs, i.e. NF Stilly, Skykomish, Green.
While WDFW has contributed to its share of fishery screwups, this doesn't seem to be one of them. They probably erred in adding the kill fishery just as ocean survival was declining, but it's unfair to feel they should have seen that coming. No one else did.