we did do factions waaaaay back when our server was very young. like dark mentioned, the mods/admins were almost all on one team. it was unfair, and rarely did combat occur. but when it did, it was just people finding our base, /sethome-ing, and then a respawn-assault until we dumped lava on their home points, and stopped playing fair.
basically, it wasn't that great. if we had a stream of 50+ unique logins a day, we'd consider such a thing. but until then? sorry, you're out of luck.