"the issuing of currency surrogates in the Russian Federation is prohibited." They may not be planning to arrest everyone with a BTC-E account, but they are saying that the Bitcoin economy is not welcome in Russia.
that sounds more like the Russian miners and mining pool operators might have a problem since it is their work that issues new currency.
as for BTC-E I wouldn't worry too much as it is in bulgaria which is part of the EU.
if Russia wanted to invade and shut them down they would have to deal with more than just the Bulgarian government.