Between this and the subtle reference to “former second-year PhD student” it makes sense that they’d have to make a public statement.
They do a good job of toeing the required line of privacy while also giving enough information to see what’s going on.
I wonder if the author thought they could leave the paper up and ride it into a new position while telling a story about voluntarily choosing to leave MIT. They probably didn’t expect MIT to make a public statement about the paper and turn it into a far bigger news story than it would have been if the author quietly retracted it.