The users should already have to remove their bitcoins from bitfinex when it was hacked a few months ago, at that time I was having a doubt that there will be something problem from the owner and that is why I preferred to stay away from there.
When it abruptly went offline for days it was a clear sign something was wrong. People should have heeded that warning and removed their Bitcoins. Nonetheless Bitfinex was the biggest exchange for liquidity, and trading in large amounts of coins was only feasible on Bitfinex. The markets of the other exchanges were too small for whales.
The whales could only choose to trade at Bitfinex or not trade at all. Some risked it and paid the price.