Meh, sounds like typical liberal BS to me.
Let me be painfully honest here, there is a tendency in the western world to want to portray whites and every aspect of our civilization as negative. Pretty much every historical event or point of view is tainted by the desire to re-interpet every culture or group of people that wound up coming into contact with, or being conquered by, the western world, in some kind of ultra-progressive "noble savage" light when it's hardly true.
Now there is some truth to the fact that stories, especially those told for purposes of entertainment, are exagerrated to make them more entertaining. There is no denying that, but at their core there is usually far more truth than lies. To be honest while racism was more prevelant at the time (and went both ways), the reasons for exagerrating contacts with backwards savages (who were backwards savages in reality) was done for the same reason people exagerrated the exploits of famous outlaws and gunfighters... it makes for a good story. Just like your typical famous gunslinger didn't really kill a thousand men (which would be the case if you believed the stories) and oftentimes had motivations other than just "killing people just because", some of the specifics of what these native tribes did were not accurate. Of course at the same time if you've ever seen many documentaries in many cases what they did was actually WORSE, in a "truth is stranger than fiction" sense.
To be honest showing a group of tribals as the bad guys nowadays is differant, the noble savages turning out not to be the expected trope, but something a bit closer to old school stories. It's no worse than a story where a bunch of quakers turn out to in reality be a Satanic Cult at the end of the third act.
The basic arguement here seems to be that primitive peoples and non-whites should be considered a "sacred cow" beyond criticism or negative portrayal. I disagree with that, and I think a game like "Far Cry 3" creating a sort of contextual satire by doing exactly the opposite of what we have trained ourselves to expect is a good thing.
In a big picture kind of way I'd also point out that a lot of the problems in the third world largely come from the whole "noble savage" mentality and how we've trained ourselves. We basically convinced ourselves that the big thing holding back a lot of countries and Africa and such was the presence of western culture and colonialism. We largely pulled out, helped rebels, and other assorted things, and in 90% of the cases we actually made things worse. We removed what stability (as borked as it might have been) from the regions, and simply saw even more horrors and depravities unleashed as tribal factions and warlords took over and started butchering people non-stop. Even guys like Mandela arguably made things worse, and he's actually in one of the more stable regions.
In making cases like this people tend to avoid looking at the glories of "tribals" with warlords and child soldiers, middle eastern tribals stoning women to death for not marrying their rapists, and one current case where a girl who was raped has been sentenced to 100 lashes for her "crime". "Wierd News" at one point was going on about how in the Pacific Rim they wanted to make (get this) cannibal Tofu, the idea being that they would take cloned or donated human flesh and use it to flavor the tofu for use in pacific rituals and so on due to the importance once placed on "Long Pig". I remember once a while back hearing about how some tribe had a couple of kids in charge of their armies in Africa that they believed were literally divine as well.
The point being is that this crap is out there if you dig for it, it just tends to be forgotten in cases like this when someone wants to make a point. The odd thing here is that if you happened to land on a pacific island chain right now that was engulfed in war, lawless enough where pirates attack ships left and right because there is nobody to stop them, what is a tribe your likely to meet going to be like? A group of progressive new-millenium hippies leading a new age "noble savage" lifestyle, or a bunch of murdering maniacs like everyone else (which also explains how they survive). In reality in situations like this there are no real "good guys", and that's what I think the point being made in "Far Cry 3" is, and why it's a Satire on modern conventions and expectations, this is exactly the opposite of what you'd expect, and also exactly what you might find in a situation like this viewed a bit realistically. Sure, maybe this isn't 100% accurate to Pacific Islanders living peacefully in some of the more civilized US Territories (American Samoa, Hawaii, etc...) but we're turning this into thirld world "warlord ville" and yeah, it's exactly the kind of insane garbage I'd expect under those circumstances. I mean cripes...
In short I find nothing wrong with "Far Cry 3" and I think these kinds of complaints are generally BS nowadays.