He can pardon her right now on the grounds of protecting national security interests from any accidental slip ups a trial might lead to/reveal.
I’m not a lawyer but I don’t think you can pardon someone for a crime they haven’t been convicted of much less one they haven’t been indicted for yet.
But if Barry wants to pre-pardon Hillary for crimes committed, while she’s campaigning, that doesn’t sound like such a bad thing to me.