Hmm. I read the drama as showing that the scientists and the educators were being used by the corporate and military interests. Because they were fixated on their "objective" sampling of the environment, their science was nihilistic and able to be co-opted by military and corporate interests. Grace resisted this to some extent, but her resistance was ineffective because in the end, knowledge was her highest value. Jake's first encounter with the Na'vi showed them to be very cynical of modernity's attempts to "educate"--there are long stretches of dialogue about how from the Na'vi point of view, it was modernity that needed the education. The Na'vi were portrayed as capitalizing on these feeble attempts to educate: you had a lot more ability to speak English on the side of the Na'vi than vice-versa, for example.
It was only when Jake, uniterested in the nihlistic accumulation of scientific samples, uninterested in corporate stakes, made a playful and living encounter with the Na'vi that a genuine possibility of communication opened.
I agree that this is a problem. I think that the film is conscious of this problem and resists it, to some extent. I came away from the film feeling as if Cameron had masterfully deployed an array of cultural archetypes and symbols in order to tell a powerful story. I think the film is emblematic of our times. Racism is certain a part of our times, and the film is not afraid to reckon with racism. But my sense was that the film is not racist, but instead carefully and probably dangerously puts race to work in the telling of the story.
All that said, I can see the argument that the film is racist. Even if it is racist, I still think that it is worth seeing--perhaps because it is racist, but in (I think) ways that perhaps can create openings for rethinking race. It's up to us to seek out those openings, to create them, even if Cameron did not intend them. Our interpretations reflect our positions, seems to me, more than the reality of the work of popular art that we interpret.