This is a pretty hot topic out here in the PNW right now!
Atlantic Salmon are compared to everything from Green Crabs to Starlings to emphasize their potentially harmful ecological impact.
The disease factor is of the most concern, and after that the challenges to habitat and the limited forage in our West Slope rivers for salmon and steelhead smolt migrating out to the salt.
The most amazing thing I discovered in my readings is that the WDFW apparently made a concerted effort in the 80's to establish a self-sustaining run of Atlantics on the Green River. They failed, and blamed it in part on the differing Pacific/Atlantic ocean conditions that the Atlantics faced.
What to do??? I'm not sure - as many have suggested, fish farming is the currently the best alternative to the indiscriminate commercial nets for a fish-hungry public. But when does the price become too high?? I'll have to agree with Juro on this one - allow fish farms, but regulate them much more closely/strictly than is currently being done.