In perspective, Baraka thought Mileena gave the Edenian/Outworld army magic to make them powerful to beat his army down and considered it betraying him and the Dragon King, but it was the inspiration Liu Kang gave to his master Bo' Rai Cho for him and the army to stand and win this battle. When Mileena realize that the army that was suppose to meet their doom have won and survive the onslaught, she truly was amazed that she controlled the most powerful army of all, but she couldn't keep the charade up, not as long as Baraka is still alive and knows the truth about her. I don't about their endings, but I bet it will happen later in Armageddon since both are appearing in there. As for the killing in the end, the one Mileena killed was a decoy Baraka sent his place, because he knew everything about Mileena as she knows everything about him too. As to say is that they both got each other in check.
conquest mode drool over how beautiful she is...