Here are some findings from the study. Just as I thought they were ignored by the NYT. They show just the opposite result than that in the paper's article.

Furthermore, we have 3 years of data,
and combining probabilities across these three data sets
did not produce a significant result. Thus, it appears that
any difference between Hsupp fish and wild fish really is
slight.
So even by the most conservative
estimates, females taken into the hatchery should have
resulted in at least 4 to 10 times as many wild-born granddaughters
as females left in the wild.
But for the simple question of whether a supplementation
program can give a single-generation demographic boost
to a natural population of steelhead trout without obvious
short-term genetic consequences, the answer in this
case appears to be yes.
Steelhead from a supplementation hatchery (reared in a supplementation hatchery and then allowed to spawn
naturally in the wild) had reproductive success indistinguishable from that of wild fish.
Note the study did not deal with long term matters. They were not tested. As to that it simply does not attempt to make a finding.