Odd assumption, to be honest. Batman is already starting to show that he doesn't believe what Clark is doing is the right thing and by the time the game starts, is actively working against him, yet in the hero achievement, they're standing side by side.
But Superman isn't a villain, at no point has he been painted as such. At odds with Batman, misguided at best, but from the presentation of the comic and the game so far, all we've seen is that Superman is still a good guy. Unless you're gonna throw GL, WW, Cyborg, Flash, and everyone else we've seen on his side under the villain bus too, which would still make that icon accurate.
While I do agree with your spoiler'd point, it doesn't change the fact that its heroes on one icon and villains on the other, so no matter what the prequel comic says, Injustice says she's a pale skinned villain.