Well, J7, I would first say that the reason that the Pope is apologizing for this Bishop is because anything that an ordained member of the R. Catholic church reflects upon him. This is doubly the case as Benedict (I'm not a fan) recently lifted the excommunication of this Bishop, when he should be condemning the man's viewpoints. The Papacy has to worry about public image as much as the next world leader.
As for freedom of speech, yes, all have it, but Freedom of Speech does not protect you from being fired from your job if you tell your boss that his wife is fat, etc.
The bishop is a representative of the whole, and I know John Paul II believed in the holocaust,
so I understand why the Bishop is being admonished if he chooses not to recant (remember, he has the option to recant and save himself from the punishment if he so desires).
Lastly I would argue that the Bishop is not being censored, but told that if he is going to be affiliated with the R. Catholic Church in the future he is not permitted to speak out about (if he had kept his mouth shut it wouldn't have mattered) that viewpoint.
Could you give me an example as to when it becomes subversive, if this isn't the case?