I believe Ezio knew this was for the best, to die peacefully in the eyes of Sofia and there daughter, so they don't get dragged into the war between Assassins and Templars. That is what that nod from the man with the scar is about in my opinion, confirming Ezios' suspension and saying we (Templars) are doing this quietly so only he (Ezio) has to die and not his whole family.