A Game of Powers
Disclaimer: I own none of the rights to any of the copyrighted characters appearing in this work, and no infringement nor profit motive is intended. Rights belong respectively to Joss Whedon/Mutant Enemy/Fox, to either DC Comics and its parent companies or to the Shuster estate, depending on how a current court case turns out, or to Marvel Comics.
The vengeance demons (yes, we know they prefer justice demons as a title, but there's no need to be all PC) that serve D'Hoffryn, Dark Lord of Arash'mahar, are truly powerful. Although constrained by the need for a personal focus, they can otherwise make almost any small-scale changes to reality that are called for by those whose vengeance they are fulfilling. Such is the power of the Wish.
Even small changes to the past can be encompassed by this power. After all, major changes to the present can be the result of minor tweaks to the events of a decade ago. For want of a nail; don't step on the butterflies - you know the drill.
Therefore, when Lois Lane wishes that Superman were only a fictional character, it is not too much of a strain for Anyanka to derail Jor-El's escape plan for his son. Although the Starchild's Destiny is too great to delay forever, the Powers That Be are patient. It is not even too much of a stretch for her to insert a daydream of what might have been in two teenagers' heads, so that there is now a fictional Man of Steel where 'before' there was a real one. If this had been all that was asked of her, it would have been just another Wish duly granted.
But this was not
all that Lois Lane wished for. She also specified that all of the Man of Tomorrow's foes and allies should similarly stay "in the comic strips where they belong". There are dozens of each, including aliens from across the known universe, supernatural beings of great power, and otherwise normal humans with a Destiny or Fate to save or damn the world. Among Superman's foes there is a mischief maker from two planes up with greater power to alter reality than D'Hoffryn's brood will ever know. Among Superman's allies is the very Wrath of God, tied to the spectral remnants of a slightly bent Mick detective. Lois herself is an ally, depending on how you look at it, and definitely is a major part of Clark Kent's first, best Destiny.
This is too big a job for the self-proclaimed Patron Saint of Scorned Women. This is not the kind of job you just call up the head office about; this is the sort of job you regretfully decline. But it actually suits the purposes of certain Higher Powers from both sides to let the wish be granted nonetheless.
So not only is Superman removed from the cosmic chessboard (at least for the time being); so too are Luthor, Brainiac, Mxyzptlk (the imp doesn't take much convincing once it's pointed out he won't have Superman to play with anyway). So too are Lois, Jimmy, Perry; Bruce, and Kara, and many others.
Some have their lives and very geneaologies rewritten by one side or the other, so that their stories will not unfold for decades yet to come. Some are manipulated so that their otherwise ordained Destinies pass them by, possibly to come around again in future generations. Others still are politely asked not to visit Earth or its plane until they are called. For Anyanka is known to be arrogant and careless; eventually she will lose her power source and be rendered human, and at that point all her past Wishes that meddled with Time will be subject to... reinterpretation, if not outright reversal.
For the moment, it suits the Powers That Be, and the dark forces behind even D'Hoffryn, the Senior Partners and others even older, and especially the keepers of Balance, to sweep the board almost clean of the more powerful pieces on both sides. They will play a slower, more subtle game, where Champions on both sides operate in secret, and sometimes don't even know what side they serve. But they reserve the right to bring those pieces back when the opportunity arises.