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Well, several Bishops have been critical of ND, so it's not fair to say that the heirarchy has been silent about the issue. Also, we don't know what has happened behind the scenes - sometimes that's more significant than comments we see for public consumption. It would have been nice for the Pope to have been openly critical of ND, but perhaps he has his reasons not to be so vocal, for now. As for divorcing ND from the Catholic church, I don't know the legalities but I see no reason why either party (ND or the Church) could not go their separate way, if either (or both) desires. I wouldn't think one episode, even one like this, would lead to that kind of split, but you never know.

I posted this yesterday on another thread but it's relevant to the issue at hand:

Vatican Officials have decried this event and called it a "scandal." Archbishop Raymond Burke, Prefect of the Vatican’s highest court, said that if we as individuals are not willing to accept the burdens of the Catholic witness to life, we are not worthy of the name Catholic.
He added, "in a culture marked by widespread and ingrained confusion about the most fundamental teachings of the moral law, our Catholic schools and universities must be beacons of truth and right conduct."
When interviewed about ND and what the Catholic Church should do, he replied:
"What it should do is have Notre Dame come clean. Is it Catholic or isn’t it? A Catholic institution, a Catholic university, cannot give honors to someone who is a promoter of things that are opposed to the most fundamental beliefs of Catholics, and so that’s what needs to happen."
When asked by Hoopes how the Church could do this, Archbishop Burke said:
"There’s an apostolic constitution, Ex corde Ecclesiae, which sets forth the requirements for a university to have the name Catholic. I think that Notre Dame has to either follow those norms or say 'We’re not a Catholic university anymore.'"Link