The handling of the JFK case with regard to the autopsy was very (very) unusual.
The body belonged to the Dallas County ME. The body was taken away by the Secret Service with some pushing and shoving involved. The decision to go to Bethesda and turn the case over to the Navy was not made until AF One was airborne.
Epsteins body is in the possession of the ME of New York County. They will not be giving it up. If it is taken by force, it will be a huge news story.
The one way around this is the religious angle. When I worked in NYC, the ME would usually defer to Orthodox Jewish refusal of autopsy and would release bodies to meet the 24 hour burial custom.
I do not believe putting forward the idea that Epstein was a practicing Jew, never mind an Orthodox one, would fly at this point, but you never know.