I think that you have probably hit the nail on the head, except I think the deal is that IF he wins, no assassination (of him or his kids or grandkids) in exchange for no prosecution. If he loses, none of the rest matters. She just isn’t going to give up on her dream of absolute power so easily.
That said, I hope that you are right about the election.
She is not ultimate decision maker. Her bosses make the decisions. When they see the numbers a week before the election, they’ll toss Hillary under a bus in exchange for Trump’s DOJ to drop the whole thing. Hillary and the Clinton Foundation are just the tip of a much, much bigger iceberg involving the world banking consortium, the Fed, the CIA, the EU, the military establishment, Wall Street, etc.