Bring a civil action to recover the funds and enforce the charter of the charity. No pardon there.
On a related note, I assume that a pardon doesn't allow the pardoned criminal keep the proceeds from their criminal activity. What would stop the Trump Justice Department from going after the assets of the Clinton Foundation if it has been used as a vehicle for a pay-to-play scheme and money laundering? If the Clinton Foundation funds are the product of an illegal act, isn't it still a crime to hold funds which are the known product of a crime? Pardons can only be given for past crimes and holding illegal funds is a current, on-going crime which cannot be pardoned because it is still continuing. Right? I don't think the Clintons can have their cake and eat it too.