In hindsight, and according to some twisted rule of the universe, the current development made perfect sense.
In the past, Khan couldn't compromise. He had to keep looking for the Nak, and remaining on Nitis would have ruined his plans. Khan had to leave, even if that broke his heart.
In the same way, Liiza couldn't follow Khan. Her species had just suffered from a catastrophic event, and her mother had even sacrificed herself during it. Liiza had to stay on Nitis and help rebuild it. She couldn't leave, not after what her mother had done.
Either option would have hurt one side, and the universe didn't give the couple any solution outside that. The current situation was no different, but Khan and Liiza had found an alternative. Neither was willing to sacrifice the other to remain together, so they both did it.
Of course, that solution couldn't have come ten years ago. Khan and Liiza had been too young, inexperienced, and unaccomplished back then.
