Exactly, a determination not to prosecute (whether Hillary or illegal aliens) would not be binding on the Trump Administration. Only by issuing a presidential pardon could Obama protect Hillary from future federal prosecution (although not for prosecution by a state for a violation of state law).
In the case of illegal aliens, Obama can’t pardon them because a president only can pardon someone for past (federal) crimes, and illegal aliens continue to commit federal crimes every day that they stay in the country illegally, so Obama can’t do anything to stop the Trump Administration from deporting illegal aliens (or to prosecute them criminally, for that matter). Perhaps the best way to ensure that once an illegal alien is deported he isn’t allowed back in is if the DOJ obtains convictions against them for federal crimes, or a plea bargain in return for a guilty plea, with the felons being released on probation with the condition that they would be violating the terms of their probation were they to step foot inside the United States again without a visa or similar legal permission. Any “sanctuary city” that failed to turn over to the feds evidence that a person that they stopped was violating his or her federal probation would be in a world of hurt.
Well, if that legal reasoning is accurate then even if Hillary is pardoned it stands to reason that her keeping her ill-gotten gains from bribery would constitute an ongoing crime. Trump could have the FBI declare that all property and money in the Clinton foundation was illegal and the if she does not hand it over to the federal government she will be prosecuted.
If she escapes jail I would be happy with her being penniless.