From what I've read about her, Mephala is purely associated with murder and strife, but not always "evil" murder. She also likes justified murder such as revenge, execution, or assassinating government officials. In Morrowind where they have a Morag Tong (similar to the Dark Brotherhood, but they're legally allowed by the government), Mephala is considered a "Good" Daedra because she is associated with assasination and taught the Chinmer how to kill their enemies secretly.
It's not really that Mephala just purely messes with lives, she enjoys it when mortals kill others, and more tactful murders please her greatly then just savagely beating someone with a club.
Anyways yeah, I think it would be possible for Mephala to manipulate a protogantist to get what she wants, that's basically what all the Daedra do. And I could see her alliging with Dagon. I mea in Oblivion her Spider Daedra are seen fighting with his Daedra, perhaps she has already alligned with him?