Very interesting article, and especially the "Regarding Flash, NoScript is your best help here, of course."
Presumable this is also sidestepped if you don't use Adobe's PDF reader, but something like FoxitPDF reader, etc.
It appears that even when JavaScript support is disabled in Adobe Reader that the exploit still works, so at the moment there are no reliable protection mechanisms (except not using Adobe Reader?).
So yet more advice to use firefox with NoScript and don't use Adobe Acrobat PDF reader