The MSB violations have nothing to do with them dealing in Bitcoin or with BTC being money. It's what they're doing with USD which requires them to be registered as a MSB. The FinCEN guidance would appear to bring services transmitting BTC only under regulatory capture, but that's not the regulation which is being used in this instance. No "new" regulation is being used to justify the MSB offence.
IANAL, but I think no - http://www.fincen.gov/financial_institutions/msb/definitions/msb.html
Before this regulatory change, (according to some bean-counters) bitcoin exchanges were "selling stuff", not "transferring money", now they are "exchanging currency".
Several of the wimpier exchanges folded right when the change happened.
http://www.americanbanker.com/bankthink/fincen-regulations-choking-bitcoin-entrepreneurs-1058606-1.html?zkPrintable=1&nopagination=1