The same person who provided the Civil War scripts also gave me an explanation on the whole Xorn/Magento mess.

First thing it is important to know is that the Scarlet Witch has been super-powered by Loki since the beginning of the Disassembled arc, which is how she got her reality alterning powers. Loki was responsible for creating the Avengers and he needed to destroy them for closure as his part of his ultimate plan with Surtur and the forge of Mjolnir was reaching fruition (in addition to keep them from aiding Thor).

So he powered up the Scarlet Witch, and tormented her with her father Magneto's death, driving her crazy and causing her to destroy the Avengers. At the end of Disassembled, Scarlet Witch used her new reality altering powers to effectively recreate her father, bringing him back from the dead in his most rational state, and later depowering him to preserve his sanity (since it's known that Magneto's use of his powers affect his mental state). In order to restore his repuation, she also created another Xorn entity, separate from Magneto, thus alleviating Magneto from any guilt over his recent attack on Manhattan.

Doom, now attuned to Asgardian energies due to his recent escape from Hell, has been tapping into Scarlet Witch's powers as part of his Project 42 scheme, the result of which is causing some of her creations to become unstable, leading to the recent merging of her House of M energies and Xorn, and Xorn's seeking out and attacking Magneto. One result of Civil War will be Doom's restoration of the Scarlet Witch's sanity and normal power levels as Doom does will not allow such a power to exist on his planet (prior to making a few big changes using her powers that will serve as a red herring that the heroes will fight to reverse while Doom preserves a few smaller changes. But i don't want to give too much away!).