Although I think the BBC was wrong in not obeying its own charter, I can't help thinking that the British government was way too keen to ensure that the BBC bent to its will. If the BBC was not a government owned operation, perhaps it would free the BBC and the government from what seems like excessive scrutiny of the BBC by their paymasters. After all, Andrew Gilligan's report was just after 6am. The government should have simply refuted the claim (if they felt such refutation was necessary) with a press release.
Investigative journalism is a must for a free and open society. I don't believe that the Hutton report represents "a serious threat to the future of investigative journalism" because the real flaws in the BBC's actions were in the reporting and not in the investigation. The BBC allowed the reporter's views to be confused with those of the expert whose views he was reporting on.
Still, I think the Blair government should show its support for investigative journalism by relaxing the laws of libel. Such a move, combined with a government divestment of the BBC would be the best outcome for British journalism.