" I thought that no matter what the % was, it was up to the board as to whether or not Eisner stays or goes. [ "
You are basically correct. Stockholders elect directors; the board elects employees
The stockholder vote is for director, which is seperate from his position as an employee. And 30% is to "withhold" your vote on his position as a director-- there is no such thing as a "no" vote in corporate director elections. Even with 30% withholding, he would still be elected as a director---minorities do not rule; yet.
However, the Board could consider 30% withheld as a strong indication of dissatisfaction with his management, and they could then use that as a reason to change his position as an employee, ie. Chairman and CEO.