They are just introducing the possiblity that no one is wholly good and that no one is wholly evil (except for the Kishin). I really enjoy this angle to the story as opposed to the typical forces of good versus the forces of evil.

We, and the students of Shibusen, really know nothing about Shinigami before he founded Shibusen. He's been around for a very long time, he's been involved directly with killing Arachne, and his rules have been to kill witches without ever explaining why they are evil. We know from the Mifune/Angela situation that not all witches are strictly evil or strictly good, they are a product of their environment. Yet from one angle, Shinigami, who's death scythes require the soul of a witch, is merely using his students to create weapons for him. Can we really say that is all that different from Medusa attempting to awaken the Kishin, or messing with Crona? Is it any different from Arachne making demon weapons or Eibon creating all these devices? We learned from Arache's introduction that both Shinigami and the Witch Queen both want her dead.

That's what makes it so interesting. We are no longer sure who is the side we should be backing.

By the way:
<3 Patty