My better half contends he will, and that Obama will pardon her as one of his very last acts as President.
Before folks get into a debate on whether or not he can since she hasn't been charged with anything, yes, he can pardon her now.
Obama can use his pre-emptive pardoning powers for Hillary.
The Supreme Court, specifically in the case Ex parte Garland (1867), laid out in its decision how a President may exercise this ability:
The power of pardon conferred by the Constitution upon the President is unlimited except in cases of impeachment. It extends to every offence known to the law, and may be exercised at any time after its commission, either before legal proceedings are taken or during their pendency, or after conviction and judgment. The power is not subject to legislative control.
Scroll to the "Page 71 U. S. 334", section 9 at this source.
When Ford pardoned Nixon he did so of all the crimes he “has committed or may have committed or taken part in”.
Here's the full text of Ford's pardon of Nixon.
Obama could use the same exact languate for Hillary.