From Wikipedia:
The Justice Department recommends anyone requesting a pardon must wait five years after conviction or release prior to receiving a pardon. A presidential pardon may be granted at any time, however, and as when Ford pardoned Nixon, the pardoned person need not yet have been convicted or even formally charged with a crime. Clemency may also be granted without the filing of a formal request and even if the intended recipient has no desire to be pardoned. In the overwhelming majority of cases, however, the Pardon Attorney will consider only petitions from persons who have completed their sentences and, in addition, have demonstrated their ability to lead a responsible and productive life for a significant period after conviction or release from confinement
Correct. But the President of the United States cannot pardon someone for a crime against a State, only for a Federal crime. The story says a Federal Grand Jury is looking into this case, but if they come up with something that is a violation of California law, for which the staute of limitations has not run, such as murder, that could be prosecuted in State Court.
Of course there is the less than zero chance that a San Francisco jury will look very favorably on these defendants.