To take the comparison a step further, and entrance hole with a larger cm2 footprint will cause more cm3 of tissue damage, thus GREATLY increasing the likelihood that the bullet will hit something that makes the bad guy stop.
Assuming equal penetration for the sake of simplicity (easy because they'll both probably penetrate all the way through and out), .45 ACP will create a wound channel approximately 62% larger in volume. However, while this number may look impressive, what matters is not how they compare to each other directly, but how they compare in terms of scale relative to the human body and its vital internal structures, a topic that was discussed in the following thread starting at post #70:
http://www.thehighroad.org/showthread.php?t=494273&page=3#post6152890
In the end, they're both small projectiles, and despite how impressive some numerical comparisons may seem at first glance, I don't think that there is a major difference in their potential effectiveness per round. There is definitely some difference, which I've more often argued in this forum when people shout "shot placement!" too loudly, but merely comparing their sectional areas or even their diameters directly far overstates the difference, in my opinion.
I carry 230 gr HSTs, but if for some reason I were carrying hard ball and I had to draw to save my life, I wouldn't feel for one second that I was at a disadvantage because I was carrying FMJ ammo. I wouldn't change a thing about how, where, how fast, or how many times I shoot.
In terms of wounding potential, relatively speaking (and assuming adequate penetration), JHP holds a far greater advantage over FMJ than .45 ACP does over 9mm, going by either of the two numerical methods described above (also discussed in the thread I linked). You may not feel as though you are at a disadvantage with FMJ ammo, but I think that you actually would be. Is the mystique of .45 caliber that powerful? There is nothing magical about that number, and it's way smaller than a 9mm that expands to 0.60" (and some can expand even more).
The differences between handgun bullets are subtle, until you measure from one end of the spectrum (9mm fmj) to the other (230 gr HSTs.)
Then they become subtle again once you compare them to the human body.
Handguns are inferior survival tools, and you need to give yourself every advantage you can. Carry the biggest, meanest bullet you can handle. Hit the bad guy as many times as you can with it, on your way back to your shotgun. When you are fighting for your life, the only force is OVERWHELMING force.
You get more rounds with smaller calibers, which can be an advantage.