No one knows yet, man.

Baraka and Mileena being in love is merely fan speculation. Personally, I believe they are just partners who rely on eachother in order to achieve a similar goal. They'd turn on eachother first chance they got.

That's why I'm excited for this game. Finally, we can now speculate on Baraka and Mileena's relationship. We could've done that in MKG. Unfortunately, their storylines weren't intertwined in that one, but now they are so we'll just have to see!