This story is obviously sourced mainly from Raphel and her friends/allies. Personally I view the FBI investigation as them just doing their jobs. In the end this wasn't really a failure on their part, assuming the innocent reason for all the suspicion was true, they investigated her as they were tasked and the DoJ ended the investigation when they realized there was no case.
I think the interesting story is the change in culture at the State Department which has the effect of getting less human intelligence. I'm not sure if that's because they want to be cooped up in their embassies because they feel less safe meeting with people in certain host countries, or if security requirements are being imposed on them. Clearly in this case Raphel felt restricted and she had no problem, but I'm not sure other State Deparment employees feel the same.
Benghazi and the Camp Chapman attack [1] are pretty good reasons why they should be concerned about security.