This is worth a read. Some history about presidents prosecuting law-breakers from previous administrations:
It certainly would not be unprecedented if an Obama Administration were to hold high officials of a prior administration responsible for their criminal activity undertaken in the name of national security. For example, former Nixon assistant to the president John Ehrlichman said that he acted for national security reasons when he approved a warrantless break-in at Daniel Ellsberg’s psychiatrist’s office; yet he was prosecuted, convicted, and sent to jail for his actions during the Ford Administration. During the Carter Administration, too, former CIA Director Richard Helms was convicted for lying to Congress, which he did for national security reasons; he was given a two-year suspended prison sentence and fined. Former Assistant Director of the FBI Mark Felt (later revealed to be Bob Woodward’s “Deep Throat” source during Watergate) was convicted for authorizing some nine warrantless break-ins of the radical Weatherman groups for national security reasons; while he faced ten years in jail, he was not sentenced to serve any time, but rather fined $5,000, and he was later pardoned by President Reagan.