The dawn of agriculture was somewhere around 10,000 years ago. Even assuming that you're right, that's (conservatively) over 300 generations of polygamy.

Sure, but their argument centers around the stone age, which ends with the development of agriculture.

The only place the stone age is mentioned is in the first paragraph of the newspaper blurb. The study itself is much more limited, and says only that sex-determined differences in lifespan appear to correlate with polygyny across a large number of species.

Do you have a link to the original somewhere? What I've seen elsewhere (I think it was Jared Diamond's The Third Chimpanzee, which is probably out of date at this point) is that male/female size ratio is also an indicator of polygyny, and that in comparison with other species, yes, humans are, but not to the large degree that some other animals are. That would fit in with the 2 or 3 wives sometimes seen in the hunter/gatherer societies more than big harems.