If you notice, it also says that cold storage got wiped out due to a leak in the hot wallet. That can't be explained by transaction malleability alone. Something had to be very, very wrong with MtGox's accounting procedures for them not to realise that they had paid out more than they should have over such a long period of time.
But why would that be surprising? Something is often very wrong with very large and sophisticated companies' accounting; however, they are large enough to handle the corrections and writeoffs that often ensue.
Given what I know about Mt. Gox and its founder, no surprise there at all. Especially given the short time it has existed.