The infrastructure and buildings are included in the price. Even by your estimate it wasn’t anywhere near a billion. I’m inclined to believe Epstein was a government asset, but the island was well within the price range of a wealthy person who wasn’t a billionaire. There are others who also own private islands.
The CIA demolished most of anything that could incriminate them. Whoever bought the island is all they got. It was probably sold at a loss to get rid of it.