I based my speculation from how C.C. seems to be currently unaffected by Lelouch's geass even if their eyes meet. It seems that despite losing her code, C.C. is still immune to geass, but of course, we can't be sure since Lelouch never gave a blatant order (and we know how dubious the technicalities of geass are).
Having C.C. step in and take a hit is not so bad, as long as she doesn't die. It will open up enough time for Lelouch to kill Rollo with his geass, and maybe more Lelouch/C.C. interaction when she gets injured. It may even make him realize that his sister complex is not the only thing that can keep him going.
C.C. dying is the worst thing that can happen in this show, no matter how well it is done.