With the amount of funds stolen by hackers being no more than the exchange's income, I think we might see cryptopia live at one point. NZ Government is looking closely so I don't think there's a big chance that owners can run with the money - they'll cover the cost of the hack which is not small. But I do believe cryptopia will return as a solvent exchange, even if it loses all credibility and needs to close down eventually it will repay all user's funds.
I like how this thread is titled "The Cryptopia Fiasco" and the second article in your link is "A refreshing example of good crisis management.