Going from memory a bit, right before the opening theme comes on she says something to the effect of, "what will the effect of his [Lelouch's] actions be? Even now, nobody knows."
From an in-universe standpoint, if you assume the narrations to be something akin to Kallen writing an exposition-laden diary or memoir, this is so trivially true of a statement as to be comical. It is not unlike asking, "What will the effect of Kim Jung-un's actions be on global politics? Even now, nobody knows." After all, among the supposed experts predictions range from North Korea being passed off with some food aid all the way to thermonuclear devastation of the Korean Peninsula. Like all clever quotes, it is claimed that Yogi Berra once said "Prediction is hard, especially about the future."
The statement makes little sense unless you assume that in the Geass universe, people are incapable of refraining from bombastic melodrama even in their private thoughts. Given what we have seen so far, I would say this is perhaps the most correct in-universe explanation.
The admission, however, is also interesting from a meta-narrative perspective, and I think this is the one it should be examined most seriously from. After all, the point of the entire narration is that this show was originally intended to be watched once a week, and thus viewers need to be briefly reminded of what, exactly, is going on, a fundamental meta-narrative exercise.
Anime has a certain grammar, just as any medium does, and along with that grammar come certain connotations. A casual viewer given the cues this show provides may well assume that Lelouch, while morally conflicted, is the unambiguous hero of the tale and deserving of a happy ending. What this little statement may be intended to confirm is the rising suspicions and doubts a careful viewer may have started to have.
After all, at this point we have been presented with at least five possible villains (Emperor, Lelouch, Suzaku, the JLF, C.C.) and no fewer than five possible heroes (Suzaku, Lelouch, Euphy, C.C., Kallen) deserving of a happy ending. Note that these lists not only contain overlap (especially if you are convinced, as I would have been in high school, that the emperor is, in fact, expounding on a good and noble philosophy), but each list contains within it characters at odds with each other. In One Piece, Naruto, or any number of Shonen-style action anime, the vocubularies of which Code Geass borrows heavily from, we would expect that today's enemy would become tomorrow's friend. That the power of belief and desire for victory would be enough to carry our protagonist. That heroes deserve a happy ending.
And yet the characters who expound moral systems (which eventually becomes just about everyone-- Even comic-relief Rival lives his philosophy) and refuse to give in to each other, we can see already that the power of friendship, debate, and passion isn't going to sway anyone to the other side of the growing war. Now, in a more traditionally mature medium this would simply be taken for granted, but in a shonen mecha anime it is notable enough that the show-runners feel the need to add that little disclaimer saying, "warning: happy, predictable ending not guaranteed."
That, or they just threw it in there to be dramatic and raise the stakes for the sake of furthering the exuberant excess which exudes from every inch of this show.