It's not that easy. How could you ever be sure that the "plus thousands" are actually endangered. You could as well shoot down an aircraft the moment the passengers have won back "control" and if you wait until destruction on the ground is obvious it is too late to shoot.
The matter is not that simple but the German ruling basically says that the government may not count lives against lives and then give the thumbs down to the side with the lower count.
(This specifically wouldn't apply to killing an aggressor in a hostage scenario, etc., it is just innocent lives against innocent lives that may not be weighed.)
BTW, German ALPA "VC" made a statement in court against the shooting down of airliners and hailed the verdict as a victory.
It is highly unlikely that at WTC scenario will be repeated as there are a lot more vulnerable targets around that are far less protected than aviation these days. We don't need trigger-happy politicians ordering lost-comm aircraft to be shot down.
(The decision was not taken by politicians but by judges.)