It does seem there is some confusion about marines placement and even that security (marines) were not allowed to carry ammunition. I wholely agree if this was the case, that those responsible are held accountable.
There is one thing about your statement though, those who scaled the walls in Egypt and Yemen were unarmed. No staff members were harmed. Both the Yemen and Egypt governments have a lot of egg on thier face from this incident, which may push them to greater cooperate with American interest for a while. How different would that be if Marines mowed down a bunch of unarmed guys? While within our rights because they were coming into what is essentially US territory, it might have been a purposeful call that unless they were armed not to shoot.
If they represent a threat (and that is for the Marines on duty to decide, not you, not me, not some politician in Washington), then they should fire their weapons. It is not acceptable that a US Embassy be 'overrun' or 'captured' or anything else by angry citizens of that country, armed or not. If the Marine officer in charge of the situation sees that they are unarmed and do NOT present a threat (in his or her opinion), then fine. If he or she decides they do, then those protesters made a fatal mistake. I do not care if they are unarmed if the Marines on the scene feel they pose a threat and kill them based on that. Too bad for them. Being stupid around US Marines has consequences.