It is a warning to Iran to clean the software more diligently. Flame isn’t the last one. But, then, if they have more than 80 points of IQ over there they already know that.
It's a whole bunch much worse than that. The WH just exposed the fact that one (or more) of the people working in Iran's nuclear facilities is a US spy. That's something that Iran will take very seriously. I have to wonder just how long our operative(s) will still be alive after this revelation.