It's not an evil thought, Feion. Don't feel that you're inherently evil for thinking that. There are a lot of clear parallelisms between (SPOILER)the Glabados Church and Christianity, and between St. Ajora and Jesus Christ. And you don't have to believe that just because (SPOILER)the truth was hidden in Ivalice, that the same goes for what we know about Jesus. And as for the Zodiac stones and whether or not they are (SPOILER)'Evil', and why they reacted differently for Malak, and Reis and Worker 8 if I remember correctly, I think that it's closer to say that the stones react to the inherent goodness or evil within the person who holds the stone. Bad men became possessed by Lucavi (and yes I think Lucavi are demons) and good folk were either resurrected or released from a curse.

About the other topic you mentioned, it makes no sense to me why the human forms(SPOILER) of Draclau, Elmdor, Dycedarg, Vormav, Elidibs all dissipated leaving behind only the Z. Stones, while Wiegraf's body remained. The only thing I can think of is they needed Alma's comment to Izlude, the one where she says she saw Wiegraf dead and knew her brother had killed him, to make sense.