The Atlantics that were "native" to Lake Ontario were wiped out 140 years ago, so any new introductions that have been taking place with very limited success will be just as foreign as the pacific salmon are. Besides, the many factors that ultimate led to the demise of the "native" Atlantic Salmon are still in place today, so why would you expect these replacements to do any better?
As long as there are alewives in Lake Ontario, Chinook salmon will be stocked, and that's exactly as it should be. Atlantics will never, EVER, be anything more than a rare novelty fish.