Suppose the population is distributed in their experience and productivity, and that you can measure these to some extent.
Suppose your field has way more males than females. This is not your fault, more of a pipeline thing, but you want to be more equal internally than the outside world is. Most people commend this kind of thing.
If you are fairly paying both genders, wouldn't you necessarily have to take more unproductive and inexperienced female engineers to reach your goal? And if you're fairly paying based on those criteria, won't the female population be paid less as you try to take on a more-than-average number of them?
I'm not saying any of this is how it ought to be, just that it seems like a typical conclusion with napkin math, and would result in these allegations while Google is actually trying to do good.
Interestingly if equal pay were not a thing, I would expect the opposite headline: That Google would pay women much more than men to work so that they could attempt to correct a gender imbalance internally that exists in the external population (software workers).