Close Quarters Combat, something our military is involved with in Iraq. When indoors, shooting a rifle cartridge that penetrates walls can result in friendly fire accidents.
Also, the stopping power of the .45ACP is proven in Iraq.
You keep the rifle cartridge for battlefield conditions where combat takes place at ranges greater than 50 yards.
I know some cops on the swat team. They had the option of pistol caliber sub guns and they seem to think there really is no difference in stopping power in an 11 or 14 inch bbl, and subsonic 5.56 mm ammo is less penetrative than a 9mm out of an MP-5