I think that much of this report was in the works long before the Bush people got onboard. After all, these are career government employees who do the bulk of the work over a long period of time (good science, if ecology can even be considered a science, is a slow process). The political appointees should have the sense to fight them, dismiss them and their ideas, and halt the reports in their tracks when they are as counterproductive as this....but that's where good managerial, not political, skills come into play.
When push comes to shove, betcha this report was written by people who are "environmental scientists" hired in the Clinton administration. Either way, the buck stops with Whitman's inability to keep her ranks in file (or files in rank).