I can understand that they may be fiat broke but how can they have fewer Bitcoins than their legal transactions indicate?
You send me 10BTC.
I lose those BTC by some means.
You ask for your BTC back.
I say I have halted withdrawals of your BTC because $PROBLEMS
You say, "it's OK, grifferz must have my BTC because trades have indicated it"
I sit on a big blue ball.
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.