Tbh I think Noel was right, killing Shiki was definitely the best thing to do after Arcueid killed SHIKI, I still don't know why Mario didn't tell her about it anyway. But even without knowing about it, killing one anemic boy would've hardly been the most serious sin Ciel ever committed and there was absolutely no reason to think he wasn't Roa's host while he was also the only candidate.
I lowkey think that Ciel protecting Shiki for so long was pretty hypocritical, preaching about redemption and then putting her personal feelings over her duty to stop Roa.