I've negotiated fairly strongly for my past H1B jobs: again, the strong job market allows this. If the market was weak, then there would be a danger that an employer would have control over whether I could stay resident, and this would provide them with strong leverage. I would be surprised if this was an intended part of the H1B program though: I've certainly never seen anything indicate that it is.
The sort of thing happening to the workers in the article is a form of indentured servitude, which is widely regarded as slavery. I don't believe it is ethical to hold this sort of power over an individual, and IMO, those employers should face jail time. I find it hard to believe a this would be designed into the H2B program.