In "The Fall of the House of Usher", reflecting on the story as a whole as an allegory, what might Madelin represent?
I have to be honest with you and say at the beginning of my answer that I don't actually believe an allegorical reading of this masterful tale of horror bears much weight. This story does have to do with evil, though, and as the narrator tries to make sense of what he observes Poe achieves an incredible ambiguity that makes the character of Madeline very difficult to "read." It is clear that there is some kind of deep connection between Roderick Usher and his twin sister. The only time the narrator sees her before her "death" is during their first conversation together, when she passes slowly by them:
I regarded her with an utter astonishment not unmingled with dread, and yet I found it impossible to account for such feelings. A sensation of stupor oppressed me, as my eyes followed her retreating steps.
Certainly her presence is enough to make the narrator terrified, though he cannot explain why. The next time we meet Madeline likewise is a piece of classic Poe-terror, as she comes back to life, though it is unclear whether she, vampire like, destroys her brother, or embraces him out of love:
There was blood upon her white robes, and the evidence of some bitter struggle upon every portion of her emaciated frame. For a moment she remained trembling and reeling to and fro upon the threshold - then, with a low moaning cry, fell heavily inward upon the person of her brother, and in her violent and now final death-agonies, bore him to the floor a corpse, and a victim to the terrors he had anticipated.
It is clear that however we read Madeline's character, she and her brother share some form of supernatural evil that brings them both to their destruction, and not just them as individuals, but the whole house, which is of course destroyed at the same time as the last heirs are destroyed. Some kind of curse has wreaked its evil and successfully brought about "The Fall of the House of Usher."