Yeah, like showing the clone troopers round up and capture them, like they did the Utapaun's. Or somthing along those lines, even just to hint of their fate under the empire, the campaign in BF2 gives you a pretty clear hint though. "We left as heroes. Years later we'd return, as conqerors."
As I said before their probably not extinct, probably slaves under the empire, or hiding on Kashyyyk, resisting in their own way... you wouldn't hear about it in the movies though, as Kashyyyk never really plays an important role after episode III so you wouldn't have an oppertunity to find out.
Not being paranoid doesn't mean someone isn't trying to kill you... or does it?