We have no evidence. It is more that Epstein knew a lot of bad things about some of the most powerful people in the country. It makes sense that they would have wanted him killed, or even that they would have wanted to fake his death to make the court case go away. People who would kill to save themselves would be just as likely to kill a drifter and give that body to the coroner, along with very clear threats to stay quiet.
Of course we have no evidence, we can only speculate. But this is exactly the kind of thing people at these power levels will do, as we know often people at this level will kill thousands of people if it suits them.