I am a moderator on an SMP server. We have a Bukkit plugin called WorldGuard that we use to set protected plots and disable PvP in certain areas. Can WorldGuard be used to do the same thing in the End?
Whilst I never made regions in The End myself, The End works much in the same way as any other world. There's no reason why it can't work that way.
People used to make all sorts on my servers version of The End and we had it set up so people would have to get their items when they were at The End (rather than walk in with them). As such, you should be able to use WorldGuard for regions.
I hope this helps, please do let me know if it doesn't work.