I believe that this is the most likely one as it costs zero effort, and they end up with millions in tainted coin funds as bonus. It doesn't matter what they do at this point, they are already being painted off as criminals, so what exactly will change for them in that regard? Nothing.

I can't see them fully refunding everything since we don't know if the servers their hot wallets operate from are compromised by the US government. If you hope for at least any sort of refund, the hope should be pointed at what's sitting in their cold wallets. But then again, we still don't know what BTC-E is going to do with these funds.

That's practically impossible. If they happen to do so, it won't take much time for the US government to chase them down, where after that we'll run into the same drama again. But even if they do end up returning, only a total idiot will make use of an exchange being operated by the same BTC-E staff.