Furthermore, if Draco was seriously harmed there is absolutely no way Hermione wouldn't have seen him to Madam Pomfrey.

Hermione is a kind, caring person with a strong moral core, a "Milgram resister" who wouldn't even cast a Simple Strike Hex on orders from a teacher. But she's not a pacifist, is she? Perhaps she could be convinced that harming someone, or letting them be harmed, was the right thing to do. Especially if she was brainwashed a bit.