The issue at hand is that Gox has allegedly lost BTC due to double-payouts as a result of the malleable transaction. So if the price of BTC on Gox is super low, Gox could decide that it's better to change the ledger such that instead of 10 BTC a person has $1000, instead of having to buy 10 BTC at the market price (~$10 000) and use that to reimburse the person.

(Granted, considering how much trouble they were having before with USD being frozen, I can't imagine that this is a feasible move for Gox at the moment.)