Back to the missing Bitcoins and the original question. Identify the Bitcoins and stop them in their tracks. Whether double spent or stolen, mine are mine and if MtGox sent them to someone else that's theft.
You're not a newbie based on the post count... you should know by now that what you suggest is impossible.
non-sequitur
But why not stop those bitcoins from being traded ASAP. If somewhere down the road a decision is made that the stolen/missing Bitcoins belong to the rightful owners and those transactions with stolen/missing Bitcoins are not valid then freezing them now would limit the damage and to argue otherwise aside from arguing as the devil's advocate is suspect. A pain in the ass for the blockchain yes but better sooner than later.
If the people running MtGox had paid closer attention to their balance sheets, this could have been possible and have caught it within weeks of it happening... but they didn't... and so now we're looking at months and months (perhaps even years) of over-withdrawals that have happened. How would you even be able to determine which were intended and which weren't at this point? You might be able to figure out a small fraction with a 2:3 level of accuracy, but it has gone on too long, and grown too big, for this kind of damage to be absorbed... all because they were apathetic to their balance sheets.
=squeak=