Possibly nothing.
This is the CIA we're talking about here. Nothing is as it seems.
In fact, if the affair began before Petraeus' appointment as DCI, its existence would have come out in the vetting process (unless Petraeus lied about it and the CIA was sloppy in doing its homework).
And it seems even stranger that the affair would have begun after the appointment considering the delicate nature of the job (she could very easily have been in the employ of the KGB or Mossad or the Chinese MSS).
This entire case is fishy.
I read that it began shortly after he became CIA director, and it ended several months ago (her husband figured it out, perhaps?). Before I read that, I had assumed they were at it in Afghanistan.