FWIW - I always exit the pop-up by never clicking the offered buttons. The X is fairly safe but Alt F4 and the right click on the systray should be safe. It has stood me in good stead so far. But then I am wary of sites and use the Library (free) for more speculative surfing. Their systems load completely clean and all apps are screwed down tight.

Ad-aware findsof most but not all of the Trojans. The code may be buried in more than one innocent file that gets used by other apps.