The fact that the Na'vi refused to trade and met every peaceful overture with violence was them condemning themselves to their fate: we were always going to take the unobtanium, but it didn't have to be by force.
There are some issues here
The movie makes it very clear that the Na'vi didn't meet every peaceful overture with violence. Yes, when the movie starts, the relationship between the human and the Na'vi is hostile. But the movie starts several years after the initial landing and it makes it pretty clear that the relationship was peaceful if somewhat strained until shortly before the movie begins. The Avatar program itself was started because things were going decent enough for a while there (and a deleted scene, which fairly enough carries less weight, shows exactly why the relationship turned sour when troops shot up a school Dr. Augustine had been running for the Na'vi)
The Na'vi had no obligation to trade their own resources so their refusal to do can't exactly be held against them. Especially when the backstory of the film makes clear it was less an outright refusal to trade but more a lack of desire for anything offered in exchange. Negotiations took place but one party never offered a satisfactory exchange so the other party rightly refused, that's not exactly a "refusal to trade" that's simply following the basic principles of trade as a concept. If I've got something you want but you can't offer me anything I deem of equal value you can't really rightfully get pissed at me because then you're just demanding I hand over my shit to you for nothing. This is also compounded by the fact that the deposit the company wanted was directly under their home, agreeing to allowing mining would have involved relocation and destruction of that home. If they found oil under your hometown would you be amenable to an oil company forcing you and your neighbors to leave and then destroy it? Especially if what they're offering you in exchange to make up for the loss has no value to you?
Finally, I get your point that what the company and Quaritch were doing was meant to save the human race. But a decision can be perfectly rational and sympathetic while still being morally wrong. However, their decisions weren't even that rational considering, as I said earlier, there were other locations to mine that wouldn't have required a destruction of the indigenous population in that area