I'm sure this is going to sound stupid, but I'm not sure it's appropriate to prosecute, even when the letter of the law has been definitively broken. Obviously, this is how it should work, but in many cases laws regarding handling of protected information are prosecuted with extreme discretion. In other words, charges are often not brought unless there is intent and/or aggravating factors, even when the law has clearly been broken as written.
Really we need someone with substantial legal experience in this specific area to comment (I won't hold my breath for that). Despite the fact that the above code is fairly straight forward, I don't feel qualified to assess the FBI's conclusion: "Although there is evidence of potential violations regarding the handling of classified information, our judgment is that no reasonable prosecutor would bring such a case," (James Comey).
I'm not addressing whether or not it makes sense to use discretion in these cases. Personally, I don't think it's appropriate and sets a double standard; it's not like someone selling drugs will not get prosecuted because there was no intent to cause addiction. That said, I don't make the rules, and I really don't think most people in this forum are qualified to judge whether she is getting preferential treatment by applying the letter of the law, combined with the way that other laws are prosecuted (and the way laws should be prosecuted). The reality is that, right or wrong, this is not how laws regarding handling of sensitive information are applied. For the record, I despise Hillary & the Clintons and will not vote for her, even though the alternative is at least as terrible.