at this point, when a single IT operator can have access to all the private keys of an exchange, that handle million of dollars, I think any exchange will ever be 100% safe. When the prize is higher than a certain amount, there is no honest man, everyone has his price.
AND, cryptos are barely traceable.
I belive the solution is actually simple.
The CEO splits the private key in multiple parts, he holds half of the key and plits the other half to 2 or more parts. Then makes copies of each part so that at least 2 copies of each part exists and splits them to other executives. Even if one executive leaves in bad terms, there should be another copy.
Alternatively, splitting the key to 2 parts, one for the CEO and one for a lawyer should also be fine.
In Cryptopia's case it seems they were holding the keys to servers... Very clever!