See item II: Who is Covered, and section V, item 10: Outside work, freelancing, and speaking engagements:
"In appearing on TV or other media including electronic Web-based forums, NPR journalists should not express views they would not air in their role as an NPR journalist. They should not participate in shows electronic forums, or blogs that encourage punditry and speculation rather than fact-based analysis."
I do agree (as does the Ombudsman) that it could have been handled better by management -- especially given that Fox "News" is involved and their obvious glee in firing everyone up on the topic as much as possible.
However, this was not actually a spur of the moment decision: read the Ombudsman's article for the history. She says, "since I became Ombudsman in October 2007, no other NPR employee has generated as much controversy as Williams." She also points out, "After other inflammatory comments on Fox, in April 2008 NPR changed Williams' role from news correspondent (a reporting job) to news analyst. In this contract position, he was expected to report, think quickly and give his own analysis – while carefully choosing his words on any given subject."