Don't forget, there will be a Yami Marik event part 3,which will likely also be the Marik Ishtar unlock event. So unless Konami goes broke, Marik will return!
(continued) But on thr other hand, if there really is going to be an original part 3, they could start we left off with good Marik in control. Then it could be about him overpowering Yami Marik for good, and then you unlock them both.