I like the concept of the war beyond a war and the key people (i.e. Dean and Sam) being almost invisible to the people in charge. It's very true to Supernatural (and to some parts of SGA -- the misfit mission). I think the tone worked well. You may want to label/name it as a separate one-shot rather than as part 6. When I read it first as a chapter, it really didn't work -- it felt too disconnected from what came before, particularly the shift into what felt like a more omniscent, shifting perspective for the narrative. When I started again and read it as a separate story in the same universe, I found it much more successful and very intriguing.