AFAIK the original story arc ended in season five, before they started writing new material. All I remember is that there was some sort of conspiracy going on within the ranks of the angels and that Castiel was a 'rebel' so to speak and that 'God had left them.' Although this was toyed with when 'God' supposedly saved Dean in one episode. As I stopped watching after the fifth season ended, I can't really comment any further. Upon googling, I couldn't really seemed to find any information on whether or not they abandoned the concept or developed it further.
Can anyone elaborate?