Everything Mark has said would say no to that theory, but I agree it seems most plausible and is really unfortunate.
If Mark was knowingly running a fractional reserve since 2011, then I think this is clear-cut fraud with jail time involved. If Mark was not aware of the theft, then it is just incompetence/negligence. He would have an incentive to inject as much confusion as possible.
It never made sense to me how the price could fall so much in 2011. But if the thieves were slowly selling off 500,000 - 1,000,000 BTC, then that would have added a lot of downwards price pressure.