Bernier gave confidential documents to his Hells Angels girlfriend. Having an affair with an underworld figure is different than having an ordinary affair.
Were JFK's many affairs national security issues? When did the US become so puritanical?
Bernier didn't "give" her the confidential documents, he left the NATO papers at Julie Couillard's place because he was stupid and forgetful (and pussy-stupified.)
You obviously won't bother to read or give credence to other posters' opinions, but many have made the point in this thread and the one in the Politics forum that even if Petraeus and Broadwell were simply having an affair, that fact (and the fact that she was probably not being monitored the way his family, etc., would be) could be leveraged by terrorists, foreign interests, hell, even business interests to compromise US (and global) security. It doesn't matter is she had connections to criminals or not - bad guys find ways of exploiting circumstances like this.
The 'fact' that he allegedly kept harrassing her after she supposedly ended things means that he had fallen for her, which in turn would have made him more susceptible to blackmail (either in the traditional form or by more insidious means like kidnapping, threats of violence, etc.) and thus putting thousands, if not millions of people at risk.
And yes, JFK's affairs were national security issues. This is not a question of being puritanically conservative as it is about not putting oneself in a potentially compromising (and catastrophic) position while fulfilling positions of incredible importance, secrecy, security, etc. Keep your dick (or vagina) in your pants until you have finished serving your country in such a vital capacity...