You raise a good point, and I would add that it's a little silly to begin with that letting her get taken has such massive consequences: the death of everyone at Last Light (probably even Jaheira) and nobody to help you at Moonrise Towers. And let's face it, if you struggled in the Isobel fight you're going to need that backup at Moonrise. Talk about kicking the player when they're down.
Unfortunately I think it's a little late for them to be redesigning how the story unfolds. All of this is unlikely to change.
