... the people he supposedly "belonged" to would have either killed him in jail or faked his death and hustled him off to a facility geared more toward continuous waterboarding than to pre-trial detention with poor suicide watch surveillance practices.
Why would those be the two plot possibilities?
Well, if he did indeed "belong to intelligence," presumably the objective was to gather information on powerful people for purposes of blackmail.
That kind of information is only useful for that kind of purpose if it remains secret (from the public, that is). Files were starting to be un-sealed by judges. There was always a possibility Epstein would decide to start talking, and not necessarily just to prosecutors who could be pressured to "leave it alone."
If he's dead, he can't talk -- and judges can probably be persuaded to keep remaining files sealed on the claim that there's now no public interest served by revealing the names of people who haven't been charged with crimes.
If he's thought to be dead but actually at some CIA black site, they can torture more information out of him than he previously gave them "voluntarily." Everything he ever saw, or did, or heard.
Those two plot possibilities seem to me to be both sufficiently titillating and sufficiently believable to make good fiction.
Of course, I'd spice the thriller up with the possibilities that he was killed by someone working for one or more of the people he got video of in flagrante delicto, or that he put his own considerable assets to use faking his own death to cover an escape from a federal detention facility, or that the intelligence agency running him helped him pull that off and took him first to a safe house and then to another, more off-the-books private island to live out his life in luxury.
But those possibilities would eventually crumble before my intrepid investigator's awesome skills and powers of deduction. And then ...
... then, nothing. Everyone but the investigator (and his or her client, maybe) would still be left wondering and speculating. Because even if the true story came out, not that many more people would believe it than if it hadn't come out.
It probably wouldn't produce a bunch of casualties among the rich and powerful.
It probably wouldn't bring down governments.
It would probably go down as just one more Paul McCartney died in a car wreck, Jim Morrison is raising horses in Oregon, Elvis is alive and living in a cabin near Mauna Loa with JFK story.
Which is exactly how the actual theories are likely to go down.
If I had to bet money on whether Epstein is alive or dead, I'd bet he's dead.
If I had to bet money on whether Epstein killed himself or was murdered, I'd bet he's murdered.
But right or wrong, I wouldn't expect to collect any winnings.