we've not seen govs really intervene.
it makes sense btc will be tied in a high profile way to 'terrorism' ... false flag or not, it could be used that way.
they tried to link bittorrent "piracy funds terror" in the same way ... unfortunately that was a few steps removed ... this can have immediate 'hey look at what these people did only because bitcoin let them.' aka silkroad + violence
http://arstechnica.com/tech-policy/2008/03/us-attorney-general-piracy-funds-terror/there is a flaw in this reasoning because of bitcoin's pseudoanonymity.
To link a false flag operation to a bitcoin transfer you would need proof of other identifying information of the person(s) involved in which case they could not be hidden actors ... i.e. wouldn't be false flag by unknown operatives (unless they managed to coerce/connive some patsies into using bitcoin for terror and then have a watertight way to pin it exclusively upon the patsies)