Answers from the director himself.
The director addresses some questions about the film here:
http://bloody-disgusting.com/news/3202946/director-nicholas-mccarthy-t ies-up-loose-ends-on-the-pact/
The gist of the article above being:
1. Annie's one eye being blue and the other being green is meant to imply that Judas is her father. (I don't understand why this is so confusing. It's obviously movie shorthand; an attempt to save the viewer from exposition.)
2. The ending is meant to be Annie's dream. Judas is not alive.
Not addressed in the article but a couple of other things I see on the message boards that I'd like to put out there.
a. For whatever reason, Glick's ghost has no power of Judas. Either you can except that or you don't. I don't see that as violating any rules that the movie establishes. The ghost clearly has limited powers. She can affect lights and manipulate video images and can have limited communication and physical interaction with "sensitives." Glick seems to be able to interact with Annie via the necklace. That's why she can throw her around and communicate with Annie in her dreams even when she's not in the house. Some people interpret the necklace as a symbol that Glick is her mother, but the necklace's point in the story is to explain why Glick can interact with Annie directly and no one else other than the psychic she brought to the house.
b. The controversial shot where Judas appears on the viewscreen and apparently not in the room:
My guess is that the director and cinematographer were trying to be cute. The viewfinder is taking a wider shot than the camera filming the room. Judas is off-camera, but since the viewfinder is taking a wider shot, he can be seen there. It's not meant to imply that Judas is a ghost.