I was surprised aswell but I don't think it's really going and "ultra holy" way. It's not very hokey and bible thumping and the angel's are certainly not being portrayed as the all-loving good guys. My spider sense tell me that Dean and Sam will be gradually pulled to opposite sides of this war (each side showing an unquestionably ruthless and vicious attitude)... big reveal about Sam... and then the brothers move back together finding themselves at the center.
In shorty I suspect the angels will be portrayed as brutal and vicious and not the ideal. The rug may even come out from under all this if we learn that Castiel isn't an "angel" at all down the road.