That's more the fault of the bad WoW writers. That in an attempt to replace the vagueness with which they dealt with the Kaldorei issues and that they are still one of their most iconic races, even if they don't like it.
They seem to solve everything by giving it more power without plot.
(or so I see it)
In W3 Malfuerion was not stronger than Trall and Elune was just another "goddess".
At that level of power Elune could be only of the Kaldorei without automatically returning the bad guys to the Horde.
Now that elune is the "older" goddess, the Horde are the bad guys, no matter how much Elune comes out and kills the Kaldorei. There is still Cenarius.