What's at stake? Bureaucratic embarrassment or national security?

Media silent when administration targets sources - Edward Wasserman - MiamiHerald.com:

There’s Thomas Drake, a career official of the National Security Agency, who faced 35 years in prison for telling a Baltimore Sun reporter about what The New York Times called “a potential billion-dollar computer boondoggle.” At stake was bureaucratic embarrassment, not national security. (The case against Drake collapsed last summer.)

Often, when claiming the right to privacy (or 'state secrets'), it is the embarrassment that bureaucrats would be put through, not national security, that is at stake. Should the American people be kept in the dark just because some bureaucrat didn't do his job and doesn't want that generally known?