Frankly, I don't have a problem with a permanent facility in Iraq, either. A private intelligence newsletter has suggested that such be established in SW Iraq, basically away from populated areas.
But in the cases of Germany and Japan, it was really more a re-establishment of prior orders (with some improvements); thus not a lengthy exercise, nor one which required a substantial troop presence.
Iraq is not quite so simple.
Germany, to an extent (though its political order was indeed greatly changed). As for Japan: at what time in Japanese history prior to 1945 did it have a political and social order similar to the one it has had since the US occupation?