Leanne was well-aware that Siuan was up to something, something dire enough that she was pushing her aside all the time, against custom (the Keeper is supposed to be there as the witness of the Amyrlin's interviews and decisions. The Amyrlin isn't supposed to meet people alone the way Siuan did except as a private woman). She remained loyal and covered up for her despite not knowing what Siuan was exactly up to. She trusted her blindly. It was her choice, and her loyalty to Siuan first rather than the Tower as a whole is the cause of her downfall. Leanne saw her loyalty as her duty and thought Siuan as Amyrlin did hers, and never ressented Siuan for what happened because it was her own decision to have been blindly loyal. The portrayal of Leanne purely as a victim of Siuan's schemes gone wrong is largely a ploy they came up with to appear to hate one another. Leanne sees Siuan has no less a victim of Elaida's wrongs as herself. It was her choice to side with her, to trust her despite not knowing what Moiraine and her were up to, and to keep trusting her once she knew what Siuan had done.