It's pretty amazing, isn't it? I think you handled the situation just fine; yanking her chain probably wouldn't have made any difference and often just ends up being interpreted as "that's an evil apostate for you," thus reinforcing the indoctrination.
Examining own's beliefs without fear or restriction is at once exhilarating and terribly frightening. It's also really lonely; that's what I'm finding anyway (thank goodness for this place). We've set out on a journey that no one we know is willing to embark on. It's a process that leads to a kind of freedom, but the bonds don't come off without scarring. Still, it does get better, with time.