I think you misunderstood the Mybitcoin's statement about the cause of the hack.
It appears to be human error combined with a misunderstanding of how Bitcoin secures transactions into the next block. Our programmer was under the assumption that one block was good enough to secure a transaction.
[...]
In hindsight we should have credited deposits after one confirmation so they would show up in the transaction history
If i correctly interpret this statements, then Mybitcoin accepted transaction as verified after the block number was incremented, not after that transaction was included in the block. This opens an easy way to drain their coins without block chain fork, especially if you know their bitcoind IP address.