It's entirely situational. If you're arming a military or even just a task for within the military, thinking about the single operator versus a single target won't work. It's the same arguement I use to deffend 5.56mm. Using a smaller caliber allows for greater carrying capacity. When going into combat, what if the extra couple of mags a soldier can carry makes the ultimate difference?
Planing for the larger scale, thinking strategically, implies that one plans for most situations rather than trying to cover every single one. Most targets aren't going to shrug off a burst of 9mm in the chest. There are, of course, anecdotal tales of bad guys soaking up smaller caliber rounds and ultimately killing the shooter, but what is the actual percentage of confrontations where this occurs? Is it really large enough to justify working around the shortcomings of the .45 caliber round compared to the 9mm round?
The other side of the coin involves thinking very specifically. Strip away all the details. Think only of gunman, target, and one shot. In that very specific circumstance, .45 is arguably more desireable.