Easy, "whistle blower protection". That is a gold mine. He can never be fired OR passed over for promotion from this point forward. He has it made in the shade.
Just like Linda Tripp or Notra Trulock, right?
Not only that, but if he has a conscience, he has pretty much cleared it and the problems rest on the shoulders of those way up above, including people in charge, going back to Clinton.
Would it have made a difference if Bush had cleaned house and a new leadership (and perhaps culture) had been installed at the FBI? Probably not - you don't turn such an agency around overnight, if he had cleaned house, we'd be seeing the results this year. There would still be a lot of the same rules/behaviors left over from clinton/reno still swirling around. I have to go with the Bushbots on this, Bush couldn't have done anything to have stopped 9/11
You bring up the whistleblower aspect, before the attacks, if this guy had raised hell, he would have been labeled a troublemaker and probably pushed off to some backwoods office and/or forced to leave. Now he can speak his mind without fear of being screwed over by those above him.