From what i'm reading this has been answered:
-ICBM's don't have the thrust to achieve orbit so every one of those missiles is coming back down.
-ICBM's have security features meaning an unarmed bomb striking the planet will not detonate, barring freak incidents.
In other words, problem solved, the X-Men saved the day.
However, I also see a lot of speculation regarding En sabah nur's intent with the missiles, which I found to be fairly obvious. In the scenes just preceding that one we are told that following the arrival of Nur to an area there is always an apocalyptic event wiping life from said area. Then, During the nuke scene we are given a lengthy speech (by nur himself) regarding how vastly superior these weapons of war are to those he used to proliferate death in his time "No more swords, no more spears, no more stones or slings, etc." His tone is exuberant, not fearful.
This coupled with Xavier's reaction of "immediately sever this connection at any cost" implies, heavily(in my mind guarantees), that Nur launched those nukes with the sole intention of sending them right back down, armed, to kill every human on earth who couldn't survive it.
This keeps in line with Shaw's plan in first class so please don't jump me saying it's far-fetched to believe that nur and his followers/other mutants would survive the cataclysm. Even if they actually couldn't, it's still just as likely that nur was convinced that they could, just as shaw had been.
It also keeps in line with plot of the whole movie: an ancient evil intent on dealing death has resurfaced in the modern era with access to unprecedented power. The two major forces that the heroes fight to keep out of his reach are nuclear weapons and Xavier's full cognitive telepathic control.