I have mixed thoughts on the issue of "girls only" encouragement in STEM and those thoughts have shifted recently more towards "less" as my own children have gotten older (my youngest are now in 9th). At this point, I really see what Nicoledad, Spaghetti, Old Dad, and Bostonian (RE situation where verbal ability far outstripping STEM ability in a high IQ female) are talking about.
I think we can separate this into two distinct things:
1) Encouraging girls to participate.
2) Creating exclusive girls-only clubs for them to participate in.
And I get the sense that your issue is solely for the second thing.
My personal take is that I believe exclusive clubs exist for the same reason single-gendered schools exist. There's a school of thought out there that boys tend to be quite dominating, and this suppresses the ability of girls to get the most out of them in coed activities.
As an example, DD's STEM lab group included a boy and one other girl. DD treated me to daily anecdotes of the boy trying to take over everything, and doing it all wrong. Supported by the other girl who saw eye-to-eye with DD, she repeatedly had to shout him down, and then the girls had to waste time and materials fixing everything he'd done. Their group returned the top results.
Whether a girls-only activity is necessary probably varies based on the personality of the girls, but it would certainly seem to be necessary in many cases - see madeinuk's post on girl confidence.
