Maybe, but maybe not. Obama doesn't like Hillary very much. But, as we saw in October when he campaigned for her, he'll still do what he can to help his party, and a conviction of Hillary Clinton will look horrible for both his party and for Obama himself.
ON THE OTHER HAND, in order to pardon her, I think he has to list the offenses. Nixon, for instance, was pardoned for all offenses related to Watergate. If something else had turned up, the pardon wouldn't have done any good.
So, the problem with Hillary Clinton is that she's criminal in about a hundred different ways. Is Obama really going to list ALL the offenses he knows of and remind everyone of just how corrupt she is? Many of her crimes had nothing to do with her e-mail server, so if he just pardons her for crimes related to it, she's still jailable.
Obama's not going to want to pardon her for anything but, possibly, that. So things that come out about her from the Anthony Weiner e-mails could still get her convicted. Clinton Foundation findings haven't even been discussed yet. Could you imagine him pardoning her for her unsecure e-mail server, activities involving the Clinton Foundation, perjury, furniture theft, intimidating witnesses, etc? He'd look like a fool!
Some say he already does.