As far as I know, the BTC-e servers are in russia, US can't have taken them and so I don't think they have any private keys at all (maybe only Alexanders one from his phone).
Why do you think their servers were in Russia? Their main domain was banned in Russia. They used to run on BTC-E.ru before moving to .com. I've heard servers run from Bulgaria, Cyprus, Panama... so who knows? And it's quite possible that whatever the feds were able to seize were just running scripts pointing to remote servers. But this still may not bode well for customers, due to the risk of future arrest by US authorities.