I think Isaac is the Benefactor. After Allison died, he just disappeared. In the seasons previews, when it showed the Benefactor walking, it was clearly a male and you heard someone say "You killed her." I think Isaac is using Meredith to make sure that the people on the list are really dead. He wants to avenge Allison, so he is killing everyone Scott cares about. Meredith isn't really the Benefactor, but she wrote the lists with Lydia's grandma, and now Isaac is using it.