You may be able to access the kill_faction command via a script. Take a look at Myrddraal's scripting thread here to get an idea of how to script, then create and run a script that reads:
Code:
script
	console_command kill_faction thrace
end_script
Console commands that don't work in the actual console do work if called by scripts, and there's no limit on the number of times any command can be used this way. For some reason.

-Simetrical