Yes, he'll stay with ITV. Whenever he is actually interviewed it's quite clear that he has no real intention of going anywhere else. Much the same as his relationship with Sony.
Syco sold X Factor, Britain's Got Talent, Xtra Factor, Britain's Got More Talent, America's Got Talent and X Factor USA as one package. They'll do the same again and the success of BGT will help X Factor.
Not that XF really needs it. For all the "crisis" is hyped up, it was still the #1 series of 2012 among its target audience of 16-34's, the most lucrative demographic in television. The success of shows like Saturday Night Takeaway and even Splash and Catchphrase is good for ITV. But none of them are delivering anything like the revenues that X Factor does. With The Voice looking more Dancing on Ice than X Factor these days, ITV won't be feeling too confident that they'd be able to replace X Factor.
My guess is that the new deal will be 2 years rather than 3. Maybe for a bit less money, or with more BGT hours and fewer XF hours. Or maybe conditional upon more involvement from Simon. But there will definitely be a deal done, even if it does take place at the eleventh hour.