You think they would have something that gross in ocarina of time?
It is actually quite plausible, and I consider all the theories proposed here to be very well formulated. Though it is true that such ideas as amputation and execution for punishment seem to be a bit much for an E10 rated game, Nintendo has been known to sneak very mature themes and content into Zelda games. Majora's Mask is about armageddon. Wind Waker shows desperation followed by destruction of an entire society. Have you ever heard the meme "Nintendo so sneaky"? Well, it is true.
I consider it likely that Bongo Bongo was in some way tied to the Lens of Truth and that he was a criminal or villain of sometime.