I've got a little idea, solving the "huge reputation drop" issue and making the headhunting a bit more attractive.
We all know, at the moment, when someone wants to rob another one and get's noticed, he receives a huge reputation drop in, let's say the NCR.
I know that the reputation is heading toward 0 in a matter of time, but when one has -6000 or so that'll last forever.
So here's my suggestion:
If a player gets a reputation drop, his name will be written on a bulletin board at the police station, or in the middle of a town, for everyone recognizable.
Then, you read the name of "loliamathief123" and decide, to hunt his head. Surprise! You meet loliamathief123 in the middle of the desert, you kill him.
You see his corpse - you use your knife on the corpse. Shazzang! You've got his head or his scalp in your inventory! Now, if you bring said "item" to the police officer in the NCR, he will declare loliamathief123 for dead and you get a nice little trophy, and a few caps or so. loliamathief's reputation in NCR will increase a bit, because everyone (the NPC) are thinking he's dead. Maybe, he get's + 3000 Reputation (but just to 0, not that it will be abused to gain reputation very fast)..
And to make the bulletinboard a bit more attractive, it has to be in a very crowded place on the map, maybe let a NPC standing there, who is yelling every few minutes that the town is searching for headhunters or so...