There are two aspects to the seal issue. The kinds of seals you're talking about are targeting specific runs and taking a high proportion. That's actually a small percentage of the seal population. If you addressed those seals, you would protect those runs, but it would not make a huge difference to overall abundance. A lot of the other seals are eating different things, including predatory fish that eat salmon. It's unclear how those seals do. We could go back to culling and knock the seal population back down, but then we'd be back here talking about the endangered transient population.
If we want to get an ecosystem back in balance, I would recommend harassment of seals that are taking advantage of artificial conditions such as the one you just cited, and allow the transients to increase in number and reduce the pen-fed population in the long term.