There is already a possibility that Superman will escape in some betrayal way in Injustice 3. There is nothing wrong with it, but it isn't good. The whole plot of Injustice indeed is to stop Superman from being an all-powerful being who deals justice unfairly, but we can do better.
Even after the events of the first game ended, Superman's followers remained hidden in Injustice 2. It was a great concept, but it was short-lived, and the two teams had to merge. The result is an epic battle, so it was cool, but I'd suggest revisiting the original concept.
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Superman and his forces should hide from the overwhelming opposition because of considerable pressure from the superhero community in this story. As Superman slowly retakes over enough insurgency cells to defeat Batman, why not let the player help him do it?
The trouble with writing Superman is that it's hard to make him the underdog. In this video, the topic is further discussed. Why not make Superman the underdog by showing the consequences of having everyone against him?
It's not that the plot of Injustice isn't good. The comic continued the story of the second game, which I enjoyed reading. There is one thing I am tired of about games: they reuse the whole "Oh no, now you're free because someone betrayed us!" thing. Try something bigger, something that makes the player feel powerful instead of lucky.
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