"Nuke the tree from orbit, it's the only way to be sure" would have robbed us of the final battle, which was awesome, but logical for the corporation.
Actually, the story makes it clear at several points (including the book Grace is holding she wrote about the Na'vi) that Pandora is a famous discovery for humanity, and the Na'vi are probably well known all over Earth - after all, if people discovered intelligent aliens, wouldn't everyone on Earth be fixated on knowing more about them?
Because of that, unleashing the nukes across Pandora would probably never be an option whatsoever because of the popular opinion backlash. Like most corporations, RDA would probably prefer to manipulate public opinion and perception as much as possible while performing whatever ethically questionable activities under the table - even if those activities are not actually illegal.
In short, one could hypothosize that Earth is treating Pandora with kid gloves, relatively speaking. Too many people on Earth know about the Na'vi, and maybe even have a positive, sympathetic view of them thanks to people like Grace. Mr. Company Man (I forget his name) looked pensive as he finally gave the order to attack. For all his bluster about making the dumb savages get out of the way, he clearly had a lot of concern for how their actions would be seen back home. He smelled a PR disaster in the making.