Yeeaaahh regulated companies that handle vast amounts of money for their customers never get into any trouble.
If MtGox were managing real money or stocks, and did what they are alleged to have done, I expect there would be some jail time. I doubt it's worth the Japanese government's time to criminally prosecute a few million dollars of new, unregulated currency-equivalent, but if they do prosecute, I'm guessing there is a serious risk of jail time here.
Bank deposit insurance is fascinating: it largely exists to prevent bank runs, which are caused by people believing they won't get their money out. Having any insurance means that people have less reason to believe there's a chance they won't get paid back, which decreases the probability of a run on the bank, which decreases the risk associated with the insurance, which decreases the amount of insurance needed.
But, yes, because it's pretty unlikely that all banks will fail at once, it's not necessary for the FDIC to have on hand a sum matching all insured US bank deposits.
There are also limits on coverage. If you keep $1 million in your savings account, you won't get all of it if the bank goes under.