A troubled frontiersman leads his team in clearing the indigenous lifeforms in preparation for human colonisation. But when the terraformers arrive, he realises that his team is expendable and their only chance of survival is to join forces with the few remaining aliens.

It sounds quite similar to Avatar. I'm not saying that's necassarily a problem, but how much did that cost to make?
I agree with dpg about trust issues. But if he is seen being good by the locals, saving them somehow, then they might begin to trust him.
I also like the Australia or US version DPG mentioned.

How, specifically, is he "troubled"? We need a reason to care for him.

Why should I care about the frontiersman, sympathize with his predicament? Seems like he's getting his just desserts, payback for what he did to the indigeneous population. He's only switching sides to save his own skin.

(Also, the story could just as well be set in the Americas or Australia whilst being invaded/settled by Europeans. Why set it in a fictional planet and time? The CGI for fictional worlds is impressive -- but not cheap.)

Why is he troubled and how does that figure into the premise?

It seems like the problem here is that the terraformers are starting their work whether his team is out of the way or not. That's really the only reason he would realize they are /expendable/.

If they are already eliminating the aliens, why would he "join forces" with them, rather than forcefully commanding them for survival? Why would the aliens trust him? Think about other cultures, whose honor would have them commit suicide before they joined forces with anyone who disgraced them.

Just food for thought.

This is a tough one because you have it all there, now it just needs to be shortened. How about this:
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"After discovering he and his team are expendable, a galactic frontiersman must team with the indigenous people's he once hunted to fight the mega corporation which now wants him dead."
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