"If women feel put off by chess unless they have their own tournaments, then they can have their own tournaments. It literally hurts nobody."

I'm not convinced that this is completely true.

The fact that there is a category reserved for women when there is no technical reason for such separation in that activity could make girls assume that women are somehow less proficient at that activity and other similar activities. That could discourage the best of them from even engaging in that activity or similar activities.

In some activities, such as power lifting, it's pretty obvious that such separation is essential as women would rarely, if ever, win at the most levels of competition in almost any age group (I don't know if this is true, for example, in the 1-3 month old category!). In these cases offering separation encourages participation.

In this particular case, who cares?! It's speedcubing and likely this girl will lose interest in the activity soon and move onto something else (or, more likely, I suspect her parents will push her into something else and drill her on that for a couple years).