Maybe it comes down to the fact that if the Govt of the day lets the terrorists crash an aircraft into an event such as the Commonwealth Games, there would be a public outcry. Of course, if the aircraft is shot down, there would be a public outcry, but maybe it would be lesser, as they could argue that they did try to do something.
The simple fact is that if a terrorist group manages to take over an aircraft, there is likely going to be major loss of life. Personally I think it best to leave it to head for it's target, in the hope that the passengers manage to regain control.
But the govt has to be seen to have tried to do something, no matter that logic says that they will have killed the innocent before the terrorists had the chance to.