They didn't know he was a spy, hence Netyiri's outrage at when he confesses that he was: "You knew this was going to happen!?!?"
This is where the scriptment was better. It focuses more on the Avatar project's interaction with the Na'vi and only shows brief glimpses of the military plot through characters a la Max (bearded science guy) and Trudy (scorpion pilot) who keep Jake and Norm and Grace (who in the scriptment has a long-time Na'vi mate) updated, slowly building the suspense until the final attack comes. But Jake and Grace are so caught up in the bustle of Na'vi daily life, and we along with them get lulled into that violent but idyllic existence until the humans finally up the ante. In that sense, it's the anti-filmed version, with us spending more time in the trees and less time on the base. It shows how even Grace is blind to the military op (and maybe just a bit too caught up in Na'vi life and her science) and Jake's rise through the Na'vi ranks is much more natural as he keeps proving himself through several trials. To answer your initial question, in the original story it's made much clearer that the entire Na'vi race are unanimously against giving the Avatars any more chances, but that Netyiri's mother, who is the spiritual guide for that particular clan, decides that Jake will be the last one they will try to show their ways.
Not only that but the whole horrible exposition on Unobtanium (Selfridge explaining the source of funding of Grace's project to her? Like she doesn't know after six minutes, let alone six years?!) is handled miles better. Also a relationship between Earth (drab, gray and dying) and Pandora is established through A. a media crew sent by a newscorp that makes tons of money off the imagery and B. an eco-watchdog (heavily on the take) that a guilty-conscience-ridden human race has attached to the Pandora project.
So Selfridge, instead of having a miraculous change of heart and mind-bogglingly agreeing to send multi-million dollar Avatars into a soon-to-be inferno area, is actually blackmailed by the eco-officer and the media crew into giving the Avatars a chance to warn the Na'vi about the final attack. Faced with a choice between letting Quaritch go through with the attack and the eco/news people getting the truth about Pandora back to Earth, he opts for a slippery compromise.
The scriptment is much more tightly woven in terms of character interaction/motivation, and it also has infinitely better action sequences (Titanothere hunt - think buffalo hunt, except with massive herds of those giant hammerhead rhinos); the Thanator (Netyiri's mount at the end) rampage is much bigger and much more menacing, and the final battle in general is much more involved and character-driven (meaningful deaths, sacrifices to save others etc, as opposed to Tsu Tse getting gunned down and Trudy's throwaway heroism) compared to the filmed version. I don't see why they deviated from it so much.
