Wow, sure is derailed in here.>>12787268
As mentioned, no SM presence necessary or likely. Exterminatus is extreme overkill as well.
1) Scout ship or rogue trader finds Pandora. Orbital scan finds large quantities of useful materials; somewhat harmful but managable atmosphere (easily terraformable) - the planet will make an excellent forge world one day.
2) Primitive xenos noted and mostly ignored. Almost all savage planets are full of non-sentient and/or primitive xenos, humanity coexists with many of them (at a distance) so long as exterminating them is more trouble.
3) Mining colony established. Natives make nuisances of themselves, not much worse than any other large native predator could manage. They are butchered where encountered, but mostly ignored.
4) Local guard garrison captain Quatarich takes out a native stronghold. A na'vi war leader unifies the biosphere of the planet and wipes out the mining colony with overwhelming force.
5) Guard regiment arrives. Burns a beachhead onto the planet from orbit. Sends down the troops with flamers and tanks, mining colony is reestablished. Maybe a sanctioned psyker is allowed to fuck with the planet-mind.
6) There is no #6, pandora is done. The biosphere is /= the entire planet, so there are not going to be any orbital lava plumes to fry nearby ships. Once they purge a continent, they can get right back to mining and kill the rest of the planet with pollution. (would make a shitty agri-world, anyway) You would probably see na'vi slave labour within a year, as soon as you get a realistic governor in charge who can overlook xenophobia in the name of profit and status.
tl;dr - Warhammer is not all that, but even the most suetastic primitive aliens can't beat a war-obsessed spacefaring race that will not back down.