No, she wants him to continue acting and deceiving them as Zero. Even though she knows how Lelouch really is and that most of the Zero persona is an act to harp of nationalistic idealism of the Japanese, she only has revenge left to live for now that her mother and older brother are gone.
To her, Zero is the embodiment of that revenge. If he gives up fighting for his revenge, then she loses too. She wants to be deceived by him, but he is brutally honest with her: He only wants her for the battles and the secks.
In short: Lelouch x Kallen can't ever work. He doesn't give a rat's ass about her besides for her abilities. She loves a man and a persona that don't really exist. Failed love is failed.