Obama will allow Hillary to survive politically (hence the NDAs agents are forced to sign in advance of throwing out the whole investigation a few months from now). But he's going to make it clear to Hillary that he knows she screwed up big-time and he's doing her a big favor by eventually deep-sixing the investigation. It must be very gratifying to have the Clintons at your mercy. Of course, there will be little reward in the end. The Clintons are not known for showing gratitude.
I'm not sure Obama has any kind of pull left. Imagine you're one of the ones investigating this (or deciding whether to take it to a grand jury). If you thought there was something criminal in all this, it would be a hell of a trial.
Perversely, Clinton's fame and position may hurt her on this. Suppose some prosecutor thinks this is an iffy case. Might they be tempted to indict anyway, just for the chance of taking down Hillary Clinton?