This is yet another one of those things that only makes sense if you assume that the World of Warcraft changes over time. Some period of days or weeks passed between when a group of heroes fought Kil'Jaeden at the Sunwell with Kalecgos' help, and when Malygos woke up and went nuts. In theory, after WotLK comes out, the Isle of Quel'Danas should be peaceful and under the control of the Shattered Sun Offensive, even though a player will always be able to go there and fight demons.

Other stuff that doesn't make sense because everything in WoW exists at once, even though it shouldn't: Kael'Thas is in TK and the Magister's Terrace at the same time. There are a few friendly NPCs that can always be found in cities even when they're also in some distant zone to help with a quest. (Aldor and Scryer leaders helping fight Socrethar in Netherstorm, or Thrall visiting his grandmother in Nagrand.) The most ridiculous example of being multiple places at once, though, will come in WotLK. If I remember what I've read correctly, Baron Rivendare is the boss of Stratholme, a quest-giver for Death Knights in their starting zone, AND one of the four horsemen in the new Naxxramas.