I should have seen the bias in the "Human Zoo" and "Science" parts of the title. They weren't called "zoos" at all. They were freak shows and they had little to do with actual science.
Freak shows were indeed unethical. They were run by the likes of P.T. Barnum and other carnival proprietors. In the days prior to TV, these shows were the only way to bring oddities to the masses. They called it education but most agreed it was exploitation and such shows were banned.
This documentary attempts to bias the viewer with anti science rhetoric. Science does have some horrific stories, but this is not one of them.