I do have a little sympathy for the position of Wendig and the like who argue that "SFC" could be just as easily a strong character who is female rather than simply a female character who is strong but I agree that's rarely how it pans out.
Where I disagree with the author though is her dismissal of strong (badass) female characters at all. She dismisses male equivalents as boring and namechecks Superman - Superman who has been selling comics since before the war, had like six films, an series of awesome Dean Cain related adventures and is probably one of the best recognised superheros ever. Sure, he may be boring. I haven't read any of the comics, seen any of the films or watched any of the TV shows. But it seems clear he's not too boring to be successful. There's no reason a female equivalent should be dismissed out of hand (Off topic- is that Wonder Woman? I know basically fuck all about her).
The core of the problem isn't in the gender split, to my mind, though sure its an issue. Female characters are put in as a sop (seriously, remove Johansson - I don't remember her character name - from Avengers. See the utter lack of effect that has on the plot) and so all that's necessary is to show they are just as good as the boys - to show they belong on the team in their own right as a character not simply the meta-textual reasons. And because the team is doing stereotypically male things, that necessarily results in her becoming an ersatz male; because scriptwriters are lazy they want to do as little character development and defining as possible in order to give the outline of a team and their job is done with the female member. She's the female member.
But that isn't the core. The core is that many films are fundamentally about males. Not to say action films, adventure films, superhero films can't be about females. But the conventions of the genre, as they currently stand, make them about males. I don't blame scriptwriters for making Scarlet Johansson essentially masculine, they want to sell films and breaking from established guidelines is a risky move. Not everything has to be trailblazing and, yes, the gender split does effectively masculinise her. But the gender split being addressed won't fully change that if the same films are being written - look at the Charlie's Angels films. Three female leads, all kick-ass badasses and extremely forgettable characters. I'm sure there are other examples.
Characters aren't divorced from setting is my point, and until the public conception of the genre expands enough to allow settings that allow female characters to have the depth of, well, she uses Sherlock Holmes - not sure how good an example he is but whatever - then nothing will change.
How to do that, though, I don't know.