A standard issue Beretta 92F (the M9) uses the same ammo as an MP5. The difference is insignificant. An MP5 has a longer barrel so the velocity is higher, but it's still a 9mm round.
Also, it looked like he was using a .38 Special lead round nose, which is a relatively weak round , with about 200 ft/lbs of energy at the muzzle. Compare that with a 9mmx19 at ~350 or a .45 auto round at ~400.
Beside that, the .50BMG is an anti-materiel round. A shooter attempting to kill a human target from a distance would be far more likely to use a 7.63x51 NATO, or a .30 caliber long action magnum (.300 Win Mag, .30-06, .338 Lapua, etc.).
[Upon reading the rest of the article, it states that he was indeed shot with a .38 Spec.]