It is now apparent that Joi Ito was an opportunistic scumbag who elevated personal gain above ethics. Good riddance to him. And good riddance to the reputation of Nicolas Negroponte as well.
Personal gain? He didn't pocket the money as far I know.
Ethics is also a touchy subject, people can't fully agree on whether taking a criminal's money to do good with it is ethical or not. So it's not as cut and dried.
He did however violate MIT policy so that's a valid reason for his resignation or even firing in my opinion.
Epstein also invested in Ito's private investment fund, which financially benefits Ito directly.
Personally I suspect Ito was more incredibly naive than scumbag, but being naive is also not a good trait for the leader of a prominent group like the Media Lab.