I don't think btc-e intends on running a wanted criminal website, they rely on seeming like a professional business otherwise other fiat partners cannot do business with them.

The domain going down was a signal of the intents of the US Government, they don't just want to fine BTC-e but they want it shut down. They can't run an exchange like this.

It's not like the pirate bay where some governments are going to have disagreements over what technically counts as piracy or whatever, it was a huge money laundering operation even if many legit users got caught up in it, there is no chance they will return.