EDIT: If you are happy to just kill them, there's a much easier way. Just go into god mode and spawn in enough zombies to kill the NPCs. Afterwards just issue a "killall" command to kill the zombies.
My original response:
I don't know much about servers. Can you safely change "PlayerKillingMode" in serverconfig.xml once a game has started? I imagine you'd need to restart the server, but I don't know how it would affect the game save, if at all.
If so, you could set it to "kill everyone" (value 3), then kill their NPCs, then set it back to what it was.
Obviously you want to do this when nobody else is on the server, and you'll want to enter god mode to kill the NPCs without dying from their attacks.