Real history has never accepted "I was just following orders" as a very good excuse for crimes against humanity. Especially in a situation where there was no imminent threat to the person expected to fulfill the order. There was no such threat upon Itachi since the dude could leave the village just fine even after performing the task and becoming a scapegoat. So, he was free to do whatever he wanted, including hitting the road (to avoid punishment by the leadership) or defending his own family and clan, one way or another.
It's quite ironic the same people who ordered such an atrocity then have the audacity to preach about their precious Will of Fire.