I think that nothing was stolen. Mark for some reasons needs to shut down exchange immediately.
Maybe it was case with SilkRoad? Maybe with MSB in USA ? Maybe other things.
Mark needs to create new exchange without past problems (new GOX). But how to make it? Hmmm we can see now how Mark is playing with public. This is his way to full rebranding. Or even better, it is creation totally new business from roots.
He said, cold storage is not missing but temporary unavailable (what does it means?) With cold storage situation is binary (0,1). He lost his cold storage or he didn't. There is no such think like temporary unavailable. So Mark is cheating like a sissy girl . It is for sure!
He want to make new exchange. So his intentions are good. I think that he will return all BTC through new GOX. For new GOX he will find mysterious investor. In fact there will be no investors at all (Mark is too danger right now). But... he have users money and BTC. By using this money and BTC he will stimulate new exchange.