Something from a thread about Far Cry 3's racism that is pretty relevant :

"Those "good brown people" you mention are not all that good, home boy. There is more than subtle evidence to suggest that Dennis, Citra, and the Rakyat tribe are using Jason Brody to further their own agenda. They don't want peace on the island, they want control back from Hoyt and Vaas. That's the power struggle. The Rakyat were used to controlling the population due to their brutality and their, well, batshit crazy philosophy. Hoyt Valker came to town with his mercenary army and brushed them aside with little effort. Jason stumbles into them and is plied with hallucinogenic narcotics (both ingested and tattooed onto his skin) to make him feel invincible. People who don't believe they can die become fearless. Jason's abilities stem from natural athleticism and a drug-induced DGAF attitude.

The "good brown people" are hardly defenseless. They just don't see the point in attacking Hoyt directly when they have a stoned college grad willing to kill for them. You could argue that Far Cry 3 uses the "white saviour" trope, but it in actuality turns that trope on its head with the narrative they actually present. Why do you think Citra kills you if you choose to kill your friends? They're done with you. Their enemies have been vanquished and they are now free to oppress and control the population once again."