The South African Apartheid was about racism. The word apartheid has nothing to do about separating races. Deus Ex using the word apartheid is not trigger worthy.
"Apartheid" is an Afrikaans word that means "Apart-hood", Apartheid referring to the South African Apartheid. In Deus Ex's case, they're using "Technological Apartheid", which is in the same vein of segregation, but just the segregation of those who are augmented and those who aren't.
People are upset that they're 'taking the racial bit out of the word apartheid', something ignorant morons view as turning a racial issue into a "White fantasy" or something.