But, in the 45s defense, there is evidence to suggest that muzzle energy isn't a perfect indicator of stopping power. for instance, the 45 seems to do much better in the real world than ballistic data would predict.
But you asked about ballistics, not real life gun fights. AS far as balistics are concerned, the 45 is really pathetic. Well, not as pathetic as a 38 special. But not very good. Not very good at all.
If you are going by muzzle energy, a .17 beats the .45.
But in the real world, that big fat slow .45 makes a big damn hole in bad guys, and dumps all of it’s energy into him. The 9mm hardball zips right through, and leaves most of its energy in the next wall.
Now, if you are upping the ante to 9mm +P hollowpoints, that is a different issue, and a solution forbidden to soldiers.