A rifle shooting handgun ammo I think is the best home defense weapon in my opinion. Has the benifits of being a ling gun, but no over penetration that rifle cartridges have. Imagin shooting at an attacker with a .308, 30-06, .300 mag, or any other typical rifle catridge. It's not gonna work well.
Any handgun cartridge fired out of a carbine with a 16" or so barrel will have considerably MORE velocity and muzzle energy than the same cartridge fired out of a handgun with say a 5" or less barrel. That said there IS a definite danger of over penetration since a 9mm shot from a handgun already penetrates deep enough that there will already be over penetration in a human sized target at home defense distances.
The only benefit really would be the ability to use the same mags as your handgun uses. Personally I'll stick with my AR-15 loaded with 31 rounds of SP .223 than a gimmicky rifle loaded with 16 or so rounds of JHP 9mm.