If anything, awarding massive rewards to stronger negotiators is a market failure in a capitalist society, in the same way that paying more to taller or more attractive people is.
1) People are people and ingrained biases and social pressures are incredibly powerful forces.
2) The amounts of money are tiny ($1,000-$20,000) relative to a large company's operating budget. It's the same reason businesses overspend on airfare and SaaS products.
3) The hiring manager isn't spending their own money. It's no skin off their back if they pay a new hire an extra five grand.
This is especially true during an interview scenario, where people largely make decisions based upon intuition and "culture fit."
Is it actually better for capitalism to pay people based on negotiation rather than job performance? Is that a settled discussion in economics? (Obviously negotiation skill plays some role in overall skill, but that's not an answer to the question.)
Anything you use to measure their job performance then becomes the metric that is optimized for. And the things you can easily measure are almost never the important things that you need out of an employee.
I would have much preferred she change their hiring policies to educate their hiring managers on how NOT to be biased against women and to NOT penalize women who negotiate for themselves. Treat women who aggressively negotiate their own salaries THE SAME WAY YOU WOULD IF IT WERE A MAN! Education, ultimately, is the answer to a long term solution. It would also help to make sure you have an equal balance of sexes that comprise your hiring team to truly level the playing field.
For a capitalist society, if you're a stronger negotiator, then you should absolutely reap those benefits, and if you're a weaker negotiator, then you have something to strive for and improve. By eliminating it altogether, I'm not sure how you can achieve sustainable, long term success. This decision also seems to undermine or belie the accolades thrown on her for being a Feminist icon in the tech/vc world. If you're trying to level the "playing field" then LEVEL it, don't eliminate it.