This is incorrect. Maged is describing what happens to competent exchanges with the malleability bug in the quote -- and it seems MtGox was not one of those.

The claimed explanation for MtGox was:
* MtGox sends a transaction
* attacker modifies the txid
* modified transaction goes in the blockchain, and bitcoin ownership changes
* attacker complains MtGox "I didn't receive my coins"
* MtGox searches for original txid in blockchain, doesn't find it  (<-- this is the bug)
* MtGox thinks they haven't paid, apologizes and sends a second, totally separate transaction of the same value

So there will be two transactions in the blockchain (Maged even says so in his post "Under no circumstance should you just issue a completely new transaction like MtGox did. That is how they lost some bitcoins"). Identifying the pairs could be very difficult as the sending and receiving addresses might be different.