You think playing as the bad guys will mean they're not mistreated anymore? All it'll do is highlight the absurdity of a franchise called "Mortal Kombat" where no one actually dies. At least the good guys have morals or a code, or some bullshit like that, that prevents them from killing the bad guys when they win. How dumb will Quan Chi look when he goes around beating up Raiden, Johnny Cage, Kenshi, and Sonya and doesn't kill any of them just because... what? He forgot? Or maybe he's so sure of his victory, he decides to tell them what his master plan is while they're lying helplessly at his feet?
The point of Mortal Kombat is to have people fight to the death. Neither NRS nor the fans actually want people in the games to fight to the death. Good luck making the bad guys not look like complete idiots.