Trump has stated he is not interested in pursuing this, but in reality it is out of his hands anyways. Even Trump wouldn't dare interfere with an investigation being worked on by the FBI one way or another, it could really cause him problems. Now, he could pardon her, but that obviously carries serious political risks too. Obama might pre-emptively pardon her, but that puts his legacy and reputation at risk, an irrevocable indictment on his judgement and partisanship. I don't think it is a decision he would make.
If I am Trump I tell my AG to follow the law. He should stay as far away from this as possible and answer any questions with something to the effect "the presidents office is independent from FBI investigations and decisions except in extreme and unique cases". You can be sure, if the FBI believes that have a case regarding her emails or her Foundation, they will pursue it. I've read books about numerous agencies in America and elsewhere, they have a pretty good reputation of doing what is right and trying to remain non-partisan.
Ultimately the worst case scenario probably ends in a fine and a plead of ignorance with no further pursuit. Of course, if Clinton keeps herself in the sphere of American political influence, she opens herself up to further accountability.
