I think that both the article's logic and conclusions are weak. I am not trying to be insulting, and if I seem so, please accept my apologies. I always want to address how we think.
First you claimed that this is the only possible conclusion. Your refutations of some ideas have merit, but are certainly not the only possible ones. Perhaps the people with political power in this country consider brown people to be less than human, but they also seem to think that all those who oppose their might are less than human. Many of these things you refer to are or have been done to all sorts people of all races when they cross the state.
In the end, if you walk down through it, the real problem seems to be philosophy. To someone that believes that the state and its preservation and "interests" (whatever those dangerous things might be) are always right, anybody who does not act as though they believe that (despite what they profess in religious settings) are a threat to the government and must be marginalized, demonized, or destroyed. And if you happen to be somebody just trying to live your life and are in the way of the actions to destroy those opposing the power of government, well too bad. We are governments, and we have the right to kill you if needed.