Given the profits MtGox is making, it wouldn't surprise me the exchange buys $1K in Bitcoins for the account holder so he has his 500K coins again.
That type of thing is maybe acceptable from a lean startup that's learning as it goes, but when you're transacting over a million dollars in trades per day, there's an expectation that you'll figure out what you need to do to get things running smoothly.
This might not be totally fair, but when I saw the .php extension on all the trade API URLs and noticed that there was a dynamically generated price chart on the front page (apparently not cached, based on how long it took to load) I was immediately suspicious of the competence of the Mt. Gox devs to handle the scale of what they'd created (or rather, AFAIK, the scale of the system that they purchased from the original creator)...I'm not really that surprised that security was completely botched, this has seemed like a very amateur operation from the beginning.
Is there confirmation of this somewhere?
1. MtGox sold 500K Bitcoins clearing all the buy offers highest first (as this is how sell orders clear).
2. MtGox is going to undo all transactions above the $1K/day transaction limit that was set for the account.