If BTC-e tries to refund customers it will be using crypto after socializing losses.

There is no way they can use wires since they would be blacklisted and after the first wire the FBI would seize the bank account the wire came from.

And even if they refund with crypto you should be very careful. All crypto wallets that receive founds from BTC-e could be blacklisted and then when you try to cash out in any other exchange they might block your accounts in order to prevent the FBI seize their site for money laundering. You'd do well to move your crypto through thousand of wallets prior to send them to any exchange and then cahs out in small chunks. At leats that are my plans if I get any refund in crypto.

By the way I don't think the FBI seized all their FIAT but they probably are chasing them through a lot of instrumental companies owned by another companies in many tax haven countries like a matrioska Russian doll. The problem is how will they can cash out their fiat and how to secure it before the FBI gets to them.

Returning the service with the charges they have is not an option unless they arrange with the US DOJ to remove the charges and register as legal MSB after paying a big fine. I think this option is very unlikely but not impossible.