Bear with me, guys, this is all fanboy conjecture.
Let's assume, for conjecture's sake, that Cable truly is Wolverine and no clone. He comes to the present with his pack o' mercenaries to kill Chuckles. By doing this, he will prevent something baaaad happening in the future. Or so he believes, since future-Bishop says he was once a great man who lost his way/is now out of touch with reality.
Many of you fans (certainly including me) fear that this will bring with it the concept of alternate timelines, something which bogged down the 616 universe (and in particular the X-books) with heavy continuity problems, or at the very least complications. However, there is a way out of this yet.
The "bad thing" that Xavier supposedly caused by his nasty little businesses on the side, as Cable so aptly put it, simply still happen due to Xavier's absence. Inaction can certainly lead to as much disaster as bad/malevolent/ignorant decision-making. I will leave this "bad thing" unnamed, since it's not really necessary for this kooky speculation.
So, following my "Xavier is now in Cable" theory, Xable (Cavier? Whatever, it's about as retarded as Gwarnage or Xorneto.) goes to the future to see whatever damaged world Cable and his mercenaries inhabit. Xavier doesn't even necessarily have to take over Cable's body. He can just act as some sort of "conscience" or whatever. Hey, if Betsy Braddock can do it...
He helps and inspires Cable and his men to become as great as the X-Men once were, and together they unite whoever are the future good guys against whoever are the future bad guys. The future is fixed within the future itself, so no alternate timeline. The past was changed, but the future still happened, like in that Denzel movie right before it got stupid.
In this scenario, you can easily bring Xavier back to the past since the good guys would be more than willing to help him out to find some comatose body for him to inhabit after his aiding them to victory, OR you could Xavier say "My work here is done, goodbyeeee!" as he does a Jedi-fader-awayer.
I would hope for Xavier to stay dead, since I kind of loathe "comic book death".
So there you have it, a dead-staying Xavier and no alternate timelines, at the expense of one arc set in the future.
I'm pretty sure it won't work out this way, btw. Too tidy for Marvel. Need loose ends, darnit!
P.S. For the supporters of "Cable is Dr. Cornelius' Wolverine clone, hence the lack of powers" => Cable does state he once did have a healing factor. I'm afraid they were setting up Ultimate X-23 with that "Wolverine of our own" line. Yeah, I know.