They need to cancel her security clearance. That should put a stop to her bid for presidency without actually indicting her.
A POTUS’s clearance is granted by virtue of the Electoral College. Qualifying for POTUS automatically confers need to know. It is his (or hypothetically her) appointees whose clearances are granted as established by statute and regulation. Also, the POTUS can declassify or downgrade the classification of anything they see fit, as they see fit.
The president doesn’t need a security clearance. BO would certainly never have gotten one. The president gets to determine who does need one though.
That system was overhauled by—Bill Clinton. Quite an interesting bit of history actually.