"There were mathematicians doing new science to make Flame work."
the government thinks that this is just like normal weapons research.
what they don't realize is that "secure-enough" crypto is far more important to the world economy than their small use in breaking it.
if a government could spend $800B and prove/create a machine that makes asymmetric cryptography impossible - and will be reverse-engineered and known to the world within 3 years of when they start using it, they probably would.
meanwhile, the world loses a lot more than $800B if you can't do anything secure over the public Internet anymore, or have to have previously exchanged a one-time pad to anyone you want a secure connection with.
this isn't just another weapon. mathematics is a public good. Of course, if you can spend $800B on new math and then break it, then in some sense it was "always broken." In another sense, however, that's not true at all. Quit messing it up for everyone.