In light of Alaska's decision to shift the responsibility of certifying salmon to an industry body, the Marine Stewardship Council issued this press release. The key point: the current certificate is valid until 2012, so the certified sustainable status of Alaskan salmon is not in doubt. MSC says:

A change of clients is permitted under the MSC program and is not unprecedented.  It is also important to note that a change of client does not affect the value and credibility of a fisheries’ certificate as a globally recognized third-party verification of sustainability.  The Alaskan salmon fishery was re-certified in November 2007 and the current certificate is valid until 2012.

As the Alaska Department of Fish and Game has stated ... their position as a client for an MSC certification is unusual. More typically fisheries clients are groups of fishers and their associations or seafood industry and commercial entities, who are better placed to directly benefit from all the advantages third party certification can bring.