Johns has New 52 Superman and Wonder Woman together before he and Lois.
Geoff Johns is a huge Lois/Superman fan. Do not assume that the current choices in the new 52 came from him. He's a company man first and foremost.
This was the brainchild of Dan Didio bc Didio doesn't understand Superman or Wonder Woman and he really has no clue what to do with Wonder Woman nor does he care about her. Didio wanted a stunt with media attention and that was what he got. He cares little for the characters. Johns is making the best of it for the time being but that doesn't mean he likes it. Ask anyone in the know at DC Comics and this is the answer you will get.
Of course, the reasons that Superman and Wonder Woman are together in the new 52 (stupid, cowardly reasons btw) are null and void in the Man of STeel universe.
Clark is in love with Lois in the new 52. He wanted Lois first. He dreamt of marrying her in Morrison's Action Comics. But he was a coward. He never found the courage to tell her the truth or tell her how he felt. He isolated himself when she tried to reach out to him. He pulled away from her out of fear and never told her the truth. Even while dating Diana, he longed for Lois, fantasized about her and continued to obsess over her.
He turned to Wonder Woman in loneliness and cowardice just like Diana turned to him in loneliness and cowardice because she couldn't bear to lose Steve Trevor. (AKA the guy she really loved.) This is how Geoff Johns wrote it. Wonder Woman was on the rebound after a bad break-up from a guy she truly loved but turned her back on. That said, Wonder Woman is a bit sympathetic in the situation. You feel for her.
Of course, it's hard to feel any sympathy for Clark since his problems are of his own making. He chose to isolate himself and he turned away when Lois tried to reach out to him and be close. He pushed her away. Anyone who reads comics or watched 10 seasons of Smallville or watched "Lois and Clark" KNOWS the answer to Clark's problem is staring him in the face. He just has to find the courage to be honest with Lois and take a leap of faith. That's it. That's the solution. But he's cowardly.
All of this is null and void in Man of Steel as Lois knows the truth about who Clark is in that universe already. Not only does she knows....but she accepts him openly and freely with no judgement. She put her life on the line for him and was willing to go to jail for him. Clark does not have to fear keeping the truth from Lois bc she already knows.
The barrier that Clark put up between himself and Lois in the new 52 that drove him to Wonder Woman out of loneliness does not exis in the Man of Steel universe and never will. Bc Clark is not alone. If you read the novelization of the movie it actually SAYS that after he kills Zod. Lois holds him and Clark thinks internally that he was "wrong" to believe he was alone....he's not alone anymore. Lois is there.
Either way, don't assume that Geoff Johns is on the Superman/WW bandwagon. Sometimes what's going on behind the scenes is a much different story.