The set of legal transactions on the blockchain is determined entirely by what the majority of miners will accept. So far that has always meant executing and verifying the transaction's script, but a currently-illegal script could be declared valid by persuading enough miners to treat it as an exception. In particular, suppose MtGox can produce an audit trail showing that a particular set of addresses corresponds to their inaccessible cold wallet, and nobody else challenges their claim by signing a message from one of those addresses. Then they could petition miners to grant an exception and have the coins transferred to a new address by fiat. (ha!)
It would certainly be an unprecedented intervention by the core Bitcoin community. But if it would restore public confidence in the protocol and economy, then it would be in enough people's interest that I think there's a slim chance it could be made to happen.
EDIT: it's not quite that simple; see the discussion below.