I must agree that you can't really say anything useful about this incident without knowing what was in the paper. The title makes it seem like an outrageous situation: "Scientists Have Paper On Gender Bias Rejected Because They Are Both Women". I imagine that what actually happened is probably a lot more nuanced.
It could very well be that the quality of the paper was rather poor. The article says the two female researchers just looked at the number of papers submitted by men and women, the number of jobs they applied to, and how long it took them to get accepted for a position. They then apparently concluded that, since women tended to be less successful, this obviously proves the existence of gender bias because the quality of the work cannot possibly be different, you know, men and women being equal and all.
I know that the article only gives a brief and possibly distorted summary of the paper, but if this was indeed the content, the reviewer has a perfectly valid point saying the results could also be explained by a lower quality of women's work. That doesn't mean that this is indeed likely to be the case, just that it would be an alternative explanation that must be ruled out before you can conclude anything about gender bias.
There have been other studies on academic gender bias, for example the one where identical papers were sent in with either men or women listed as the authors, and noting the discrepancy in their acceptance. And yes, a bias did indeed show up there, so I certainly don't rule it out, but you have to use proper methods instead of jumping to conclusions.
The remark about including a male co-author is obiously not a very smart one, but I kind of understand the reason for that suggestion too: a paper on the Palestinian conflict written by Jewish and Palestinian co-authors is more likely to be neutral than a paper written by only Jews or only Palestinians. So for this particular issue, having a male co-author is probably not a bad idea. Especially if they jumped to a conclusion about gender bias without ruling out alternative explanations, which would actually suggest gender bias in their work.
Once again, I haven't seen the paper so this is all just speculation on my part. The reviewer certainly could have phrased his comments a little better, though. Maybe he was just poking fun at them for writing an obviously flawed paper, but it clearly didn't get interpreted that way.