I think you're forgetting about this guy
http://www.11points.com/images/zelda...yesofskull.png I used to hit him on purpose to manipulate game RNG during speed runs.
and then there is always the Cucco. I do get your point though
Semantics aside though, those people are trying to summon the omega weapon and bring havoc down on eorzea, to not engage them and destroy them before its a threat is allowing Eorzea's demise. There have been numerous times where we've engaged NPCs and killed them when they threaten to harm yourself or an individual. The gladiator quest, the main story quest (when they were going to frame the person for the bread), puglist quest, numerous encounters with the syndicate in the past, and etc. In addition we have no quarells with killing Garleans, whom are humans just trying to rid the world of primals, however we have a quarrel with humans trying to bring the destruction of Eorzea and murdering leaders while confessing to it at the same time? I see no difference in this except we've actively just watched them murder someone of high power in eorzea and threaten to balance all of it. Far worse than what the garleans have done to Eorzea, barring Nael.
The brass blades and crystal braves gave zero fucks about engaging us before, I don't see why now they would think us the good guy. In fact the Crystal Braves were the ones that poisoned the sultana and both the brass blades and the crystal braves were the ones that framed us to begin with. All of the crystal braves that held loyalty to the scions were disposed of they said. So all of the ones that wear the cloak at this point are in with the syndicate/new leader.
With regards to an adventurer poisoning the sultana, didn't the lalafell say that the syndicate were going to pin the blame on you and that he was going to do his best to dispel it because people wouldn't believe that the warrior of light would do such a thing?
edit: Also since the Azure Dragoon did not want to fight, how did he return to his senses suddenly? He was completely possessed by Nidhogg. . .