The truth is that although in Injustice we are told that the SM side was the bad bad guy, the truth is that the BM side were not saints either. BM tried to use Trigon and the Gods to attack SM, Kal many times forgive him and even so Bruce kept attacking him, Bruce the only thing he wanted was to return to save his city but with the Regimen that was impossible. I have always seen that the two sides of Injustice are the bad ones. if Bruce had helped Clark to be more moderate and less dictator, many lives would have been saved instead he simply decided to declare war on him because what Batman says is the right thing to do.
but the saddest thing about this game is that it has drastically damage the image of both SM and WW as individuals and of course SMWW too