The gist was that the Allies were planning for the worst, and their original occupation orders and rules of engagement included some pretty harsh counter-measures. Public execuations, for example, not only were in the playbook, but actually happened, including of a 16 and 17 year old pair accused of recording and transmitting U.S. troop movements (to whom?!).
Very quickly, within months, in both Germany and Japan, it turned out that such orders were not required to keep the peace, and a process of scaling back the authority of individual unit commanders to dispense justice was curtailed.
In passing, the author contrasts this with what happened in Iraq, where our side was convinced we'd be treated as liberators, and, just perhaps, [ed: I'm mentioning this crime, not mention in the article] crimes like looting were virtually ignored, rather than some sort of deadly penalty enforced.
The article doesn't mention that the Bush administration put incompetent lackeys in charge of Iraq, while the same can't be said for Truman, Eisenhower and MacArthur's actions in WWII. That never helped, and it would be nice to see Bush spend some years in jail just for that.
Still, it seems like a good basis for arguing the Bush administration was too nice after the invasion, principally, of course, because they thought they were the best things ever, and figured everyone else shared the same view.
Melissa Willard-Foster, "Planning the Peace and Ending the Surrender: Deterrence in the Allied Occuptions of Germany and Japan" Journal of Interdisciplinary History XI.1 (2009) 33-56