TR and marine,
You are strawmanning the argument. No one is arguing that a bigger bullet permits one to be less accurate. In fact, I will argue the bigger the caliber, the greater the recoil; thus, less accuracy, which is a negative factor. But, ignoring that and confining the argument to bullet size alone, all else being equal, a bigger bullet is more effective.
A bullet does not wound on the basis of diameter or radius; it wounds on the basis of cross-sectional area. Perhaps the best metric for comparison is volume of tissue damaged per unit length of vital tissue traversed. In the case of a FMJ .45 that is 0.1605 in^3/in; for the FMJ 9 it is 0.0993 in^3/in. The metric simplifies to in^2, or simply the cross-sectional area.
There can be no doubt that two identical wound paths, one with a .45 and the other with a 9, the one with the .45 will impart more damage, precisely 62% more. A bad guy with a .16-in^2 hole in his heart will almost certainly bleed out faster than his twin with a hole in the same place, but only 0.0992-in^2. Neither will live long enough to dictate his will, but the guy with the bigger hole will very likely bleed out faster.
Now, from my perspective, other factors have led me to choose 9 Luger over .45 Auto, specifically, less recoil (thus, greater accuracy), and far greater capacity. In terms of wounding potential, my 15-round CZ 75 Compact chambered in 9 Luger exceeds that of an 8-round compact 1911 chambered in .45 Auto. But, don't fool yourself and others by falsely stating that a bigger FMJ bullet does not make a bigger wound, which, all else being equal, is more effective.