Think about what you just said a bit more.
You realize how many examples there are in the game of this sort of thing that totally contradict what just claimed was a loophole?
You clear an instance, and roll on the loot. But the next time you go to that instance, all the enemies and bosses are back, and sometimes the same unique loot drops more than once. This is a restriction on gameplay, not lore. You're supposed to pretend it's not happening and ignore it.
Then we have Outland and Northrend existing in the time period they took place.
Then we have Kael'thas being in both the Magister's Terrace and Tempest Keep.
In an MMO like WOW, there is no present time that pervades in all places, unless you're role playing around it some way.
They would not need to remove the Black Temple if Illidan comes back, The Black Temple happened in the past. The Scenario shows it in present/future.
This sort of thing should never and will never prevent Blizzard from developing future lore content.