I am sure there are times where economics in a capitalistic society is racist. But I do not believe that is the case in this instance with Facebook. No one has yet proven that they are discriminating against a group of people. That would require that you come up with information which told us how many Native American's are actually being discriminated against. The articles name maybe a dozen or so people effected by this policy (which is rather low I am sure there are more than that, to be fair). Let's assume that all of these people were Native American and do some back of the envelope math to see what percentage that effects.
World population = 8,000,000,000
Native American population (2010 Census) = 5,000,000
Facebook users = 1,400,000,000
Percentage of world users who are Facebook users = 17.5%
If an even number of people across all nationalities use Facebook this would mean there are: 875000 Native American Facebook users, give or take.
That means that: 0.0014% of Native Americans are troubled by this policy according to those who have stepped forward in these articles.
Of course there are probably many many more. 10 times more? That would be 0.014% of all Native Americans. 100 times more? You get the idea.
On your second point you state that if Facebook designed an algorithm... are you sure they checked every possible cultural naming norm when they designed the algorithm? I do not believe they did. Does this make them discriminatory or racist? In fact, no. The real question here is, do the update their algorithm to become smarter and better at allowing in real users and keeping out fake ones? The answer here is yes. That would make them the opposite of racist. In order to be discriminatory, you must actually discriminate.
Facebook does discriminate. Look at what they do to small businesses that do not pay for ads and only want organic (read: free) advertising. They are very open and public about the fact that they do not care about and do discriminate against these small business individuals.