I don't recall negotiation attempts? Even if they occur in the storyline later then what's been implemented and they refuse or ignore they shouldn't be mistreated. An example: if terrorists hijacked a boat and refused to negotiate, they don't lose rights.
Ignored negotiations are taken from official
storyline: "Some nations attempt diplomacy, sending messages in a thousand different languages to the aliens ravaging across the countryside. Their words are ignored. Within hours, all three cities are emptied of human life."
Human terrorists are at least capable of negotiation because of their human nature. To my mind, negotiation is a must if a mutual coexistance is to be achieved. Ability to negotiate makes the difference between SkyNet and Matrix machines. And XVI is more of SkyNet type - both were artificially engineered for military purposes, but gone out of control and for both of them the only acceptable form of coexistance with humans is their enslaving.
ANY entity capable of cognitive thought should be given human "rights"
This point is the most arguable to me. You consider the terms "human rights" and "moral" to be all-sufficient and universal through all possible sentient life forms. I consider them to be sorts of behaviour rules that humanity agreed upon to optimize our social attitutes. E.g. do not kill in order not to be killed yourself, help the weak in order to be helped if you become weak too, etc. And these are based on our historical experience of human vs. human interaction, so adding some intelligent indederminate in current relationship scheme would eventually require tweaking our moral principles.