Looks like she's had enough, I don't blame her. http://www.cnn.com/2003/ALLPOLITICS/05/21/whitman.resigns/index.html
I don't think she ever really liked being there. And not just the rumors about her being at odds with the White House - I don't think the EPA really appealed to her.
Anyone could've told you it was a mistake putting anyone from New Jersey in charge of anything having to do with the environment.
I seem to recall that she wanted the dredge the Chesapeake Bay to clean it out. Which sounded good but there was a debate on whether doing it would kill off the endangered Blue Crab population.