If He Can't Have It, Then No One Can
Whatever Doctor Manhattan had planned for retconning history, it apparently doesn't work, as his future vision shows him. Manhattan considers two possibilities -- either that Superman kills him, or that Manhattan himself kills Superman, along with everyone and everything else. A rather dire prediction, either way.
Given that Doctor Manhattan has the power to traverse realities and alter history, it's unlikely that even Superman has the capability to destroy him -- if his moral code would even allow that in the first place. Manhattan's latter and more apocalyptic scenario is the more likely of the two, and not hard to extrapolate from his current position.
Manhattan abandoned his own world at its darkest hour, so he's clearly not above throwing up his big blue arms in defeat. As he becomes similarly disillusioned with his new world, the notion that he would also give up on this one isn't unlikely. Does he perhaps think, as Ozymandias once did, that destruction is the means to salvation?
Salvation, or …
Perhaps Doctor Manhattan has come to realize that abandonment isn't the answer, and that he's now willing to go to more extreme lengths to save the world, just like his former colleague. He was, after all, more than willing to allow Veidt go through with his genocidal plan, so hatching his own plan of mass destruction isn't that far-fetched. But what kind of weapon of mass destruction could he use to accomplish such a large-scale feat?
How about... himself? In a potential nod to Zack Snyder tweaking Alan Moore's original script in the 2009 film, Doctor Manhattan himself could be the self-destructive weapon needed to set things right. Manhattan's final vision shows what appears to be himself exploding -- a decidedly apocalyptic move that might have been the very thing Superman was trying to prevent in his vision. But, considering the nature of his powers, such a move by Manhattan wouldn't necessarily be purely destructive. It could actually end up serving as the means to save the world.
One of the more unique aspects of Manhattan's powers is that his consciousness exists across time, not just in the present. It raises the potential question of what exactly would happen to him if he were killed. Would he just cease to be, like anyone else? Or would his death reverberate through the duration of his existence? If he were to die, might he just disappear across time?
If so, his death could indeed be the very key to saving the world, and he just might have come to realize that. If Doctor Manhattan's destruction results in his erasure from existence, then he never would have existed in the Watchmen's world. He never would have ventured to this one. He never would have allowed Alan Scott to die. No other heroes would have been removed from history. Nothing would have stopped the Justice Society of America from forming.
All that which has been retconned away by Doctor Manhattan's intervention would now be free to stage its own… rebirth.
Such a continuity-altering conclusion is the hallmark of a typical DC Comics event. Its apocalyptic ending would also follow in the tradition of Watchmen's own startling climax. And perhaps, most importantly, it would redeem the character of Doctor Manhattan, who would go down as the hero who saved the DC Universe -- both literally and figuratively.