I imagine Mileena would still eventually be introduced but would the circumstances be any different? Kitana having obeyed her father's orders would surely have lived a lot longer as perhaps the villain with a heart? Or would she have formed an alliance with Mileena and Jade as her ending suggests to overthrow Kahn and become protecters of Edenia?
I think that she would of at least formed an alliance with Sindel who may have wavered her decisions had Kitana stayed loyal to Kahn and co. Perhaps Mileena would not have come to be if Kitana had never found out about her, only of course if Kitana had regained her father's trust.
Maybe nothing would have changed accept for Kitana just delaying her turn to the good side, Jade may have opted to stay as a body guard to Mileena?
I'm not entirely sure but lets get your thoughts?