Why expect anyone to leave the show? Just because it happened in the first season, that doesn't mean it's going to recur. The consensus of reviewers, with which the producers seemed to agree, was that the first season was hampered by its dependence on the Vandal Savage/Hawkman/Hawkgirl arc, and the actors in those roles were considered somewhat disappointing as well. So the producers dropped them and adopted a new format that was more about stopping time aberrations than having a single overriding mission, and it's been working well. And the actors playing Nate and Amaya seem to be working out better too. So I doubt the producers would be inclined to get rid of them.