Ok firstly this is a very old known problem, Secondly it effects those sites doing transactions that are not managing their transactions properly. Mutating transaction may be a bit harder than you may think. It is a problem on the bitcoin protocol. But it is one that can be resolved, this is not a fundamental problem, Mt. gox is using this as an excuse and crying like a baby.
In short The fault is at Mt Gox side for faulty implementation of the wallet.
All Mt gox had to do was to implement a code on their side to track a mutant transaction.
I'm not just talking about Gox. This is a well known problem for sure. But as an attack vector today someone (more aptly a group) could just decide to use the same strategy to bring the system to a halt. I'm kinda sure (not statistically speaking because there is no data to back such things) that most exchanges use txid to track transaction. It has been the way for quite sometime.
So if I wana get an exchange to stop (and assuming most exchanges use the above approach - its not a naive assumption to make ) :
I start withdrawing, change transaction sigs (yea it maybe harder but with such stakes involved will only make it easier) , mutating the transaction, resulting in a different hash and there you have it .. transaction malleability. The particular exchange is in serious trouble.
Now I don't discount the fact that other exchanges who do this right will get away even after such attempts.
BUT
What amazes me is why have there not been attacks using such an attack vector ? Or maybe I missed it somewhere .. does anybody know of such attempts in the past ?