The Petreus incident is sort of crazy for this reason. Here is the head of the CIA, doesn't even use PGP.
There are other mixnets such as Mixmaster and Mixminion that do what Tor does for TCP but with email. They unfortunately need many more people to run nodes.
He's just a bureaucrat, hired after retiring as an Army general. I seriously doubt if he had any personal spy craft training beyond "use this secure computer and this secure phone when you're working on company business, sir. And don't talk about Fight Club."
The head of the CIA is aware of the methods used to extract information from suspects, and thus wants his information to be easily found if he's discovered, rather than requiring him to be extra-ordinarily renditioned and water-boarded.
</tinfoil hat>
I guess it just shows that anonymous and private communication is still really hard for most people, even though we had the work of cypherpunks trying to help.