Well I suspect two things:
#1: Right now we have a strong pro-censorship goverment that is attempting to jump all over gaming. Whether people want to believe it or not, consider that the "Hot Coffee" fiasco had people from both parties involved but perhaps the biggest ring leader was Hillary Clinton (look it up). Hillary is now in a federal cabinet position.
The changing wind in the US (going from making noise to more definate pressure) has of course emboldened other nations as well. Australia and Germany for example have tightened their laws on video games, largely I feel because it's not like anyone can point any fingers with the most free country in the world moving towards the same things.
Basically it IS stupid, but Modern Warfare is the bad boy of the moment that gets attention.
Besides which, right and wrong CAN be matters of perspective. To put things into context, while your character in Far Cry is doing some things considered conventionally bad, it can (and has been) argued that outside intervention through helping to maintain water pipelines, provide medicine, etc... simply creates more problems within an overpopulated part of the world. The idea being that if we were to say let Africans die by the millions due to disease, poverty, drought, etc... eventually the population would reduce itself over a few generations as "Cruel" as it would be, but the reduced population would be fitting within what the resources of the region could support and sheer survival would probably deal with a lot of the other issues in the region such as factional violence.
I don't articulate it well, but over the years I've read some rather pessimistic analysis of when doing the right thing can actually be the wrong thing. Especially when you look at discussions of human overpopulation, and how fighting some of the symtoms simply drag things out and make them worse over a period of time.
Of course not being a shooter fan, I haven't played much "Far Cry" so I could be wrong as to the attitude and some of what is being said. I'm just guessing. Personally if I had to pick examples of "bad" they would be the various sandbox crime games (which HAVE gotten complaints). In those games it pretty much says flat out your the bad guy, and half the "fun" of the game is to randomly commit acts of violence and terrorism to see how the world reacts.
#2: I wouldn't be surprised if Infinity Ward is actually responsible for a lot of this at the same time and is intentionally baiting/feeding the media somehow. It after all gets attention for the game. The very fact that any sane person looking at this in the context of gaming realizes it's fairly mild as far as such things go, is part of why I suspect it was set off intentionally as part of a marketing campaign.
After all consider a lot of gamers enjoy the potential to be bad and seeing things "push the envelope". Hence discussions on the level of content in "Fallout" through the years, and talk about "what you can do" in various sandbox games.
Truthfully, any rational person would have gone after Prototype earlier this year if they were looking for a victim. You can say more about that game being "just plain wrong" than you can about Modern Warfare 2 where the protaganist is at least serving the greater good.
For example in Prototype the game gives you an achievement for rapidly killing people, and encourages you to eat innocents for more power. It also sends crossed messages (as people like Yahtzee have even commented on) where despite killing people left and right the protaganist still makes pretensions of somehow being the good guy. The scene Yahtzee painted in his review of the protaganist running people over on sidewalks using a tank and going "gorsh, I seriously hope I'm doing the right thing" was 100% accurate.
In Prototype your NOT a CIA agent your a bloody sociopath's personality adopted by a murderous virus.
... and honestly I'm cool with Prototype. I mean to me it has the whole "Godzilla" thing going for it (and honestly, nobody watching those movies is actually cheering for the military or the poor squishy people getting crushed as the two monstrosities do battle).
So in short for those who read this far, it's both political, and probably a matter of the company poking the politicians to get some free press. I'd suspect the contreversy has a lot to do with the number of units they have moved.