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.)