Shor's algorithm is very tasty, but when the real world demonstrations at top research facilities are saying, "yes, we factored 21 into 7x3, but WITH ENTANGLEMENT"[1] it makes me think that scaling to RSA-size prime factors is still a good way off.
Listen, the US government is powerful, but building a full scale quantum crypto decoder ring in complete secrecy _decades_ ahead of everyone else? I just don't think so. Maybe I'm a sheep for not wanting to believe the government so powerful and corrupt, but the whole thing sounds like a tin foil fantasy.
I don't doubt they would if they could, though. And they've done as much as they can with present day tech: supercomputers, mass data collection, penetration of target systems, exploiting SSL's many weaknesses, tapping undersea lines, and legally strong-arming perceived threats into giving up their encryption keys. I just don't think we need to get science fiction involved.
[1] http://www.nature.com/nphoton/journal/vaop/ncurrent/full/nph...