I assume a kinetic bombardment is imminent: http://en.wikipedia.org/wiki/Kinetic_bombardment
The scriptment fills in some of the gaps though. First, corporations are banned from using weapons of mass destruction in space. Second, the planetary consciousness convinces the humans to leave and not return by threatening them with a virus that will kill all of them.
I have to say the exact same thing occurred to me at the end of the movie. "And so the aliens returned to their dying world." ...yeah, to get more ammo.
Of course, the counter-argument might be that the Na'vi managed to defeat a heavily-armed base using a skeleton force, before most of the tribes had even turned up, so by the time they got back Pandora could be too well-prepared to resist for them to be successful. Kinetic bombardment is all very well, but you need to get down to the surface to pick the stuff up -- unless you completely destroy every living thing on the planet, in which case you develop a very serious logistical problem (they were growing their own food on the surface).
An interesting interpretation, but not one born out by the film. Remember this is a private corporation, so they likely have laws back on Earth they must answer to and it is likely that would ban such an overt destruction.
A "forced relocation" (and remember that for whatever reason they did try to drive them out with minimal loss of life at first) could likely be justified under their laws, and probably so can preemptively wiping out a massing army that could overwhelm their security with shear numbers. Kinetic bombardment to wipe out huge swaths of the population probably crosses the line.
Also, it would not be surprising if they did not actually have space based weapons. They had to jury-rig a transport to act as a bomber. Its quite possible that either the company does not have them at all or that they have to travel all the way to earth and back (a many year journey) to get them. And of course, that still only makes sense if their laws would let them use those space based weapons.
I do wonder about the modern press applied to historical situations (WWII, American Frontier).