Another thought which occurred, is that Amelia Bones killed Narcissa in revenge for the Death Eater's killing of her family members, then Dumbledore claimed responsibility in order to send a message to the Death Eater's and Malfoy to discourage further attacks on the Order's families, and prevent Lucius from finding any evidence of Amelia's responsibility, which might have allowed him to remove one of Dumbledore's more powerful allies. He probably would have had to have been careful to give the impression that he would be willing to do so 'again' to the other Death Eaters if he wanted them to stop, though, unless Lucius cares a lot more about his allies than shown so far, or at least made some threat against Draco, who Lucius seems to care about.

EDIT: I was wondering how killing Lucius' wife would provide leverage over the other Death Eaters when I realised something rather obvious in retrospect, Dumbledore is the Headmaster of Hogwarts. He already has plenty of leverage, doesn't he? If need be he can hold all the school age children of Death Eaters and their allies hostage, or expell them, denying them good education and potentially giving them a bad reputation. If the parents withdrew the children and sent them abroad though, they could grow up without the knowledge of local politics provided by a hogwarts education (including personal knowledge of everyone important in your age group, which in such a small society, not-having would likely be a big disadvantage.)