Mtgox uses a proprietary version of the code with modifications that suit their needs, however due to shoddy workmanship and failure to update their client to be line with current standards, there is no malleability issue strictly speaking.
In realizing their problem they decided to profit off the issue by falsely announcing a bug in the code...the bug is theirs, not the standard code. Their public announcement was a stunt which has put them in disrepute by those who have an understanding of what happened. Also you'll find that they fail to mention how much $$$ they made by causing market panic and huge price shifts. This is one of the reasons many developers are actively pursuing decentralized exchange solutions, to avoid market manipulation on such a scale. If BTC-E was to have "problems" the market traders would panic and it would result in only profits for the exchanges as they profit not really from price but from volumes.
Perhaps someone else can weigh in.
i'll read the article but i doubt there is much to their unfounded announcement.