Unless a betrayal comes up. In the few times Malekith/Malerion has come up, he's been stated as working alongside Sigmar. He even designed the training grounds for the Stormcast, where they can beat each other to near-death and come out without any permanent injury.
Add to that, I doubt GW would shift all the dark elf armies to a new Grand Alliance.
However, Morathi's fate is still up in the air.