Question is, why are not internal transfers frozen also? I've asked this on #mtgox, because this could leads to more negative balance account and was given "if you think so" answer.
I can think of tree reasons (four actually, they weren't aware of this route and they will freeze internal transactions also):
1. The whole teory is wrong and there's something else going on.
2. The number of coins stolen is just to small and they don't care.
3. The number of coins stolen is just to big and they don't care.