This is a special blog dedicated to the character of Neytiri, I'm a fan of her myself, she is my second favourite character in the film, after Jake of course.
The fact that her sister was gunned down right before her very eyes along with a lot of Na'vi youngsters makes it easy to sympathise with her, and to understand her resentment for the humans on Pandora, and also why the Omaticaya in general view humans as demons who bring nothing but death and carnage to their land, and they're sick and tired of it all.
When Neytiri sees Jake, an intruder, a Sky Person, wandering around in the Omaticaya's territory, wielding a huge, wooden spear, she assumes that he means trouble and plans to kill him, not in cold blood, but in defense of her land, but when the Atokirina tells her that Jake is pure and means no harm to her people, she no longer expresses any desire to kill him, and even protects him against several viperwolves, although she is furious with him for causing her to kill them. Despite praising the strength of his heart and his fearless nature, she demands that he leave. The fact that she allows Jake to come to Hometree after another sign shows that she trusts Eywa with her life, so much so that she is even willing to put aside her own feelings to obey Eywa's wishes.
After falling in love with Jake and mating with him, only to discover that he was an RDA mole and knew the whole time what they were planning to do, imagine the deep amount of betrayal she must've felt in this moment. Neytiri, who has resented humans since the death of her sister, has grown to love a human who appears to be different from the other humans, only to to find out that he is supposedly just like the rest of them: determined to bring destruction to her people. Her home is blown to smithereens, a large number of the clan is dead, and she is forced to watch her father die right in front of her, reminisce of how she saw her sister killed, and then there's Jake, the one she sees responsible for everything, sat right next to her trying to offer her comfort, the nerve she must've felt he had to even talk to her let alone touch her.
When she witnesses Jake's triumphant return as the sixth Toruk Makto, I can only imagine the amount of relief and happiness that Neytiri must've been feeling in that moment, that Jake was truly different from the other Sky People and truly cares about the Omaticaya, and his love for her wasn't a lie. The shame and remorse in her eyes for her previous treatment of him as she explains that she was afraid for her people before Jake came back and gave them all new hope.
Neytiri was the right person to kill Quaritch, he is the one responsible for (quite possibly) the death of her sister, the destruction of her home, the scores of Omaticaya were killed, for her father's death, and now he's trying to take her mate away from her, so it was right that she got to exact her revenge on Quaritch, even if she didn't know who he was.
I think it's safe to assume that in the sequel, the chances of another breakdown in their relationship are zero, as Jake no longer has any skeletons in the closet and is now the leader of the clan, why would she suspect for even a moment that he would betray the clan? Especially after everything they've been through, and seeing Jake in his human form was the defining moment in the begining of a new chapter in their relationship, she accepts him for who and what he is, Sky Person or not.