I am really suprised that it took them this long to complain.
I am from Bolivia and have mostly followed this game, not because it really interests me, but because of the whole "It is in my country" thing. Basically, I have watched the trailers, read some articles, and watched some gameplay (so its clear that my knowledge of it its just superficial)
To be honest my inital reaction was "A Ghost Recon set in Bolivia, cool!" and i was impressed with the landscapes and the overall geographical depiction of the terrain since i would say its fairly accurate to what can be found, even if its a little exagerated on some aspects. They even showed one of our traditional dances (the costumes were kinda funny looking but ok)
It really did not bother me, or even sparked an inner discussion of: Should this be bothering me? Perhaps it is because I am very used to Bolivia being depicted in a rather negative tone most of the time, not only by foreign media but also our own (Most of our cinema is a clear example of this). Hell, I showed the footage of the trailers to friends and family and nobody complained (they all just laughed whenever a cholita could be seen in the background)
Nevertheless i would say the context of the game is clear: A mexican cartel is taking over and the rural population cannot fight back, enter "ghosts with guns". Really, it is such a standard fictional setting that no one could take it seriously or link it to the real context of the country.
Having said all that, the part that really saddens me is that the minister is probably making all this fuzz as a political move, rather than an earnest attempt to improve the depiction of our lovely country.