I'm defining remnants as either adults that have reproduced successfully or juveniles that were born in the wild.  I don't question that this has not happened, but whether these occurrences will develop into an established run.
Stinkfoot, your right, there has not been much research done; I think Volpe's stuff may be it.  I base my opinion on the 20 years of opportunity that Atlantic salmon have had in Puget Sound and BC to establish populations that can be considered true "runs", and they haven't.  Its established runs of fish that will cause serious ecological disruption to native steelhead and salmon populations.  A few successful spawners here or there, in a stream here or there, won't harm the ecosystem.  
The fact that you have any exotics reproducing at all is alarming to some, but to me, 20 years of trying indicates that its not going to happen.  
You bring up another good point regarding the tiger muskie, which is sterile.  Folks have developed sterile muskies, sterile steelhead (triploid rainbows), and sterile brown trout; they could probably engineer sterile Atlantics, which would make this conversation moot.  
The disease issue is significant, although there is no evidence that diseases are being transferred to wild populations.  The Canadians are studying this in the Fraser delta where many of the net pens are located. 
The baitfish issue is interesting, but again it seems to me that they can find alternatives to using actual baitfish.  What do hatcheries use?  I read the article that Land Tuna is referring too and its put out by the commercial fishing industry. Hmmm
Just like agriculture, net pens have environmental consequences.  But if farmed fish satisfies a demand that would otherwise by satisfied by wild fish, there is a net benefit.  As always, a balance must be struck, and it is my opinion that the regulation of net pens into extinction because a few spawning Atlantics have been found is unnecessary.  Especially when there is the potential for real positive benefit to wild fish.