Charles knows nothing.
I am getting the distinct feeling that V.V. is operating independently of Charles and is moving for something larger than what Charles thinks is actually happening.
V.V. seems to act to Charles in a similar way C.C. acts to Lelouch, except V.V. enjoys his own position of power as the leader of the Geass cult. C.C. is probably no better, and is merely using Lelouch as a tool to be cast aside later once she achieves whatever goal she has.
Cornelia might be learning that something truly horrible is occurring and that both C.C. and V.V. are enemies manipulating the field. She might forgive Lelouch for what he did if this turns out to be true, seeing him as nothing more than a pawn of C.C..