As the
Jargon File write-up notes:
"from Vietnam-era U.S. military slang via the games Doom and Quake"
But, eh, we should recognize the actual origin here. "Frag" is short for fragmentation grenade. It's the kind of grenade that kills by shooting splinters of hot metal--fragments--in all directions. As opposed to, say, phosphor grenades. (These kill by extreme heat and fire, which they are uniquely engineered to distribute. I had a teacher once, of Lithuanian origin, who bore huge scars on his legs...told me a live phosphor grenade he found on a beach not far from his home as a child was responsible. This was in the '40s. He called it Adolph's gift.)
But frag, as a verb, came into popular usage during the Vietnam War. As in Charlie Sheen's line from Platoon: "I say we frag that fucker tonight!" He meant murder his commanding sergeant. As in kill him with a fragmentation grenade, a readily available weapon.