Those SR2 coins came up missing/stolen at about the same time, did they not? Who's to say Mark didn't have something to do laundering those for them? And using his customer monies to do so would not be legal or ethical, as he's not paying interest. But maybe $0.10 on the dollar was too tempting for ole fatboy.
Furthermore, the malleability issue is known for like 3 years and had been on the Wiki for 1 year. So suddenly when the SR2 coins are known to be on the move, it suddenly becomes an issue? Give me a break! He may well have laundered those coins from SR2 and used transaction malleability as a cloak for the laundering. The whole thing stinks to high heaven. But it's a familiar stench coming from GOX, given their previous escapades. These guys are dishonest players.
Remember --
Mark Karpeles isn't in Japan because he's Japanese. He's there for regulatory arbitrage. Never forget that. He KNEW the price was going to fall because of his announcement. And he no-doubt took advantage of his ability to move markets with his announcements -- regardless of the fact that it was a 3 year old known issue of limited significance to any exchange who tracked internally properly.
TL:DR
He may well have shorted BTC using his customers' coins/money, AND/OR laundered SR2 coins.
I'd bet $100 Mark knows EXACTLY what happened here:
https://blockchain.info/charts/bitcoin-days-destroyed-min-year?timespan=7days&showDataPoints=false&daysAverageString=1&show_header=true&scale=0&address=