If btc-e are still in control of coins they cannot turn them into cash because fbi will have easy job to trace them.
But if they allow users to withdrawal their coin they can put a limit of 100-200 USD a day and a different address each time and they will be able to withdrawal their own coins.
Think about it more than 100,000 users with multiple addresses each will be the biggest mixer of all time.
Considering that hackers won't keep coins in a exchange for long because they want to cash out asap then 99% of users funds are legit so if fbi will try to verify each address and each user will cost them more than they will be able to confiscate.