As noted earlier, I don't think the aformentioned ending sounds anymore disturbing than the one featured in The Last Stand . . . a woman mercilessly tearing scores of people apart piece by piece (in what can be described as Hell on Earth) only to have a man struggle to approach her while she rips portions of his flesh off with her mind . . . moreover, to have that same man plunge three claws into her chest/heart, while watching her as she dies in front of him . . . Anything can be written to sound disturbing--it's another thing when it's actually shown.
Also, the statement regarding the Dark Phoenix Saga not being able to carry a movie on its own, wasn't made by Arad until after X3's pre-production debacle. The Dark Phoenix Saga is certainly capable of holding its own as the main plot of a movie, especially if one goes so far as to further expound upon it's themes, as well as introduce new villains and dynamics such as the Hellfire Club, etc.