You're probably right that a well-placed individual at the FBI could stymie an investigation, and certainly could steer it in a particular direction. (There's nothing wrong in principle with an investigator judging the appropriate direction to pursue. That's his or her job, but the decision should be based on the evidence.)
But I also think that any connections with a foreign power or with al-Qaeda would necessitate the involvement of the Defense Dept. At the very least, Rumsfeld would be kept informed of the status of the investigation. Also, the Defense Dept., the State Dept., the CIA, and the NSA are more natural places than the FBI to put together information on the anthrax case (assuming that it is, in fact, a foreign military action).
I don't doubt that either incompetence or a mole at the FBI could disrupt the FBI's investigation. But this would not stop the U.S. government's investigation, since that is likely to be centered in defense and foreign policy areas.
Even if the FBI is more competent and trustworthy than it appears to be, the Defense Dept. would be foolish to rely on what is essentially a domestic police investigation in trying to unravel a foreign military attack. And Rumsfeld and Wolfowitz are far from foolish.
I'm also very reluctant to talk about a foreign agent manipulating the FBI without some sort of proof. Idle speculation on such things is problematic at best.