I think the show has always played with the idea of the trinity in one form or another; Sam, Dean and another. John was the God of the first season, the journal was the 'bible' he left them. The way Dean laid his hand on it in Wendigo was very suggestive. Then there's the number of times Dean introduced himself to people and they responded by saying "God!" One time he even replied. "it's OK, you can call me Dean" :) Then Sam stood in crucifix pose before he dropped himself into the cage in Swan Song. I see Sam, Dean and Castiel as another manifestation of the trinity, too. And Sam, Dean and Bobby, of course. I think perhaps the person who stands in that third place is a reflection of the state of their relationship. There's a video and story project by a Russian artist and writer/translator you might find interesting. It explores similar themes about the divided God: http://semarinan.livejournal.com/1316.html