But for your example one could easily use the player order for deciding for excommunication or not.Old or new? I note that the way the rulebook is structured suggests that you should use the old turn order (i.e. before adjustment based on Council Palace). Specifically, the Vatican Report is described in section C and End of Round, including the turn order change, is in section D.
I'd personally prefer the new turn order. Also, since deciding last is advantageous, I would prefer deciding in reverse turn order.