Does the $1000/day limit apply to withdrawing to the Bitcoin network in addition to the bank options? If not the thief could have just send the 500K BTC to one of his Bitcoin addresses, and laundered the money and traded if for real currency at his leisure. Mt Gox can only roll back trades within their system, not transactions involving the Bitcoin network once they're in the block chain.
Yeah, I thought this as well- why the hell, if you had access to all the accounts, you wouldn't just take all the coins.
But- mtgox is the main exchange (handles 90% of volume), so how would you launder the money elsewhere? There just wouldn't be the volume to get it out. Also, everyone can trace bitcoins- if you took them, people can see what you are doing with them. I think this was possibly the easier, surefire way to go.