Man this story is awesome and terrible at the same time. The Mane 7 are Defeated, TIA, Twilight, and Cadence are turned to stone, Shinning Armor might be a pile of Shadow Crystals now, and the entire Crystal Army are Shadow Crystals now
Alternatively they could be setting it up that Luna isn't around at all during important events because she secretly is still bad and helping those bad things happen.
That would be a amazing twist.... but since she is so awesome that would feel like a kick to the stomach.