I agree with you on the reclassification thing. I think croaking or not after the spawn is more indicative of relatedness than protein structure. That still leaves us with three groups, of course: Pacific salmon, "true trout", and char.
Interesting link about those Lahontans. From other reading I recall that the death knell for the big fish in Lake Pyramid was the damming (I think for the logging industry) of their last spawning river. The thing is, people knew what they were doing. There was great attention paid in 1938 to the last big spawning run of 40 lb trout, and then they went and killed the stream knowing that it was the end of those fish.
One of the trout writers, I think Montgomerie, believes that there are strains within a species which have different potentials. So, while there are Lahontan cutthroats, the strain that had the potential to reach 40lbs is gone and no amount of habitat restoration can change that. He feels the same about the Rangely Lakes brook trout, which now never exceed 6 lbs, though they were once common at 10.
This is one of my worries about the way we manage stripers. If we kill all the big fish and then give them permanent irrevocable sanctified no-kill sportfish status, there may still never be big fish again.