Sorry this is long.
There are three axes of gender at play here, and it does no good to confuse them.
Axis 1. Stories written by women.
Axis 2. Stories with female protagonists.
Axis 3. 'Girl' stories.
Axis 1. Stories written by women. This is probably the most important/dangerous axis from an editor's point of view, in that, if I were editing today, I'd be very concerned about my own unconscious biases. Numerous studies (and books analyzing the studies) have overwhelmingly shown that in today's society, both men and women consistently and constantly give preference to men in the marketplace. There are some minor exceptions (i.e., in erotica, it's a bit easier to get published with a female name), but by and large, editors are people too, and influenced on a deep level by prevailing social paradigms.
This is a hard bias for editors to admit to, because consciously, you may be trying very hard to be unbiased. But it's critical to realize that your conscious efforts are almost certainly inadequate -- and probably woefully inadequate to the task. In this arena, the unconscious mind wins.
Given this, if I were editing today, I would make my first pass on reading incoming submitted material a blind pass, stripping off all author names, and would do whatever automation of process that was necessary to make that possible. (Yes, I know this is somewhat onerous -- the thought of actually implementing it makes me groan a bit. And yes, this is easier to automate for those editors who take electronic vs. print submissions -- but it can be done for either. What it requires at the print level are reliable volunteer(s) to strip the names from manuscripts and create a tracking sheet for materials before passing them on to the editor.) At this point, I consider blind evaluation a minimum professional standard for combating the deep and pernicious gender bias in our society, and would strongly argue for it in professional situations across the board -- hiring employees, promotions, etc., to whatever extent it's practically feasible.
Note: Some editors may then choose to revisit the stories (after an initial blind read) with names re-attached before making final rejection/acceptance decisions, in order to balance possible 'name weight' issues with non-discrimination practices. An editor may well decide that a slightly weaker story by a big-name author, for example, is the best choice for their publication, or that a story by an author they enjoy and trust deserves a second or third read before rejection. I consider that an understandable compromise practice, although it should be handled with some care.
Axis 2. Stories with female protagonists. This is a greyer area, since it's not a question of active discrimination, but rather a question of encouraging diversity in the material you present. I consider this a purely editorial decision in some ways -- if Jed, for example, decided that he just preferred stories with male protagonists, and wanted to publish only those, I'd say that was entirely his decision. I'd have no problem with a magazine titled 'All-Male Adventure Stories' -- as long as a proportionate percentage of the stories submitted by women were being published by the magazine. I.e., if one-tenth of the submissions are by women, roughly one-tenth of the published stories should also be by women. (If they aren't, then there are two possible explanations: editorial bias in a non-blind editorial process, or women just don't write male adventure protagonists as well, which I find implausible, but can at least be checked for using a blind process.)
That said, speaking purely as a reader, I prefer to read some fiction with female (people of color, queer, etc.) protagonists, and am more likely to enjoy a magazine/anthology/book that features a mix of characters that seems at least vaguely representative of my own experience in the real world, which is highly diverse. Does that mean I won't read a book that's all about white men? Not at all -- if I were reading Horatio Hornblower stories, given the historical time and setting, I would find it completely appropriate that the stories center on white men (though not necessarily straight white men :-). But allowing for cultural specificities and other valid reasons why an author might choose to focus on a particular gender (ethnicity/orientation), I both prefer reading diversely, and am a member of a diverse readership that would like to occasionally identify closely with the protagonist of a story. A canny editor will likely take that into account when choosing material for publication, and publish stories with a wide range of protagonists to appeal to a broad range of readers and reader tastes.
Axis 3. 'Girl' stories. Which we are currently defining (apparently) as stories putting a high priority on emotion/characterization and putting low-priority on (though not necessarily leaving out) cool whiz-bang ideas and future tech. I have a lot of trouble with this labelling method. While I do, personally, tend to prefer stories that prioritize emotional and character development, I think labelling them 'girl' stories is a too-convenient shorthand that may actually reinforce pernicious gender stereotypes.
Some women write very characterization-heavy stories, yes -- so do some men. And vice versa. I strongly resist the idea that female (or male) writers tend to write one kind of story over the other -- and even if they do, that may be a temporary cultural construct, and/or artifact of the publishing market. In any case, I don't think it's an editor's responsibility to try to compensate for that perceived, possibly imaginary, correlation. Can we just talk about 'characterization' stories vs. 'idea' stories, please?
With that gender-neutral framework in mind, it seems much easier as an editor to simply say that I would want to publish stories that provide the strongest presentation of emotion/character *as well as* idea. If forced to choose, I would probably choose an 'characterization' story over an 'idea' story, unless it really was a superlative whiz-bang idea. But that's just a matter of personal taste, and if a magazine wants to focus on idea stories, and has a readership devoted to them, then as long as axis 1 and 2 are addressed appropriately, then axis 3 should be left entirely up to editorial/readerly discretion.
And that's my two cents on the matter.