...Except that he didn't care what happened to her. If it was something important to the overall plan, it would have been told, but all Lelouch included in the plan was to use the Geass on Euphemia, make her shoot him and make him look like a martyr. He wanted to "eliminate" Euphemia, as her plans for the SAZ were in dangerous conflict with those of the Black Knights. What did he mean by "eliminate"? Certainly not pardoning her and letting her go her merry way; that pretty much defeats the purpose (he can't make himself a martyr but forgive Euphemia). He could capture her, but I have already given the problems with that. He can't use her as a pawn against Cornelia since Cornelia can't really do anything except stop soldiers (remember, as Viseroy, she can not simply hand over Japan since Japan does not belong to her).
You are correct in saying that the point of the Zero Requiem was to have all the world's hatred fall on Lelouch and with his death (by "Zero"), have the world focus on peace. However, there was also a side plan. The Zero Reequiem was suppossed to make people, in essence, forget about the massacre that Euphemia caused and clear her name. Lelouch dying does not stop the world from hating him but rather stops the world from hating each other. In the same way, Euphemia dying at Fuji did not stop people from hating her. Her death did not take away the hatred that the Japanese had for her. The Japanese were going to hate her no matter what happened to her. However, with the Zero Requiem, the Japanese turned their focus away from Euphemia when they eventually find out that she was not at fault for the massacre; it was Lelouch.