What makes you think that Director of the CIA would have particularly secure e-mail setup?
So, either Petraeus was a blundering fool, or there exists no privacy for anyone...
I'm guessing that Petraeus was no blundering fool.
He was appointed to the CIA directorship after a career in the Armed Forces, where one would not have expected him to gain such security skills.
Also being head of an organization does not imply that one necessarily has the skills to do the work of the organization.