This is often expressed in WW by Diana (or another Amazon, if they're off island) getting her toga in a twist by a simple act of courtesy like a man opening a door for a lady,
Which is a gendered thing based on men doing stuff for women because they're weaker; I mean, I do it myself because it's considered polite, but that's the source of it. It's not considered routine for men to open doors for each other.
or a woman asking a physically stronger man for help with a problem.
The scene with Diana, Steve, and Etta in the office was a perfect example of this.
Hey, Princess...mortal females aren't as strong as you are!
Except that scene clearly shows that Etta could do it herself, but is indeed doing exactly what Diana points out.
Violence against female characters is only one version of the misogyny of comics and you know it. Women in Refrigerators is not simply about villains doing violence to female characters, Gail Simone's list as often includes the depowering of female superheroes
WiR has some good specific points, but the list when it includes stuff like that casts far too wide a net, without context, and ignores similiar situations for male heroes.
(didn't that happen to Ms. Marvel,
Certainly, her history has rough patches (the editorial/writing mismatch of Avengers #200), but that's not WiR by any reasonable stretch. She lost her powers for a time, but it had nothing to do with any male character; if anything, it was setup for Claremont to introduce Rogue, a female hero, and Carol spent a few years in the X-books as an unofficial team member and badass normal, before becoming (as with many a Claremont female) uber-powerful (so powerful, even, that writers had a hard time using her, and Busiek ultimately brought her down to more reasonable levels in his Avengers run).
Hrm...not that I can think of (though that was part of Claremont's original ending to "Dark Phoenix", which would've led into another arc that would have written her and Cyclops out of the book; an arc that was eventually completed with Madelyne Pryor instead).
and Wonder Woman for extended periods at various points in their histories?)
A rather dire creative period, but nonpowered female characters like Emma Peel were very popular at the time and the writers were trying to jump onto the trend and fix a book that wasn't doing well; there's a tremendous amount of nostalgia for that period in many quarters, but it's just not recognizably Wonder Woman (which is actually rather interesting, when you think about it; a revamp of a corporate character like that today would never in a million years begin by discarding so much trademarked iconography).
something male writers do because female characters are seen as disposable and manipulable plot devices rather than fully fledged characters.
Sometimes, sure; but in a Spider-Man comic, for example, his supporting cast, male and female, is all there to service drama for him, not the other way around.
You can use a "popularity" argument if you want, but it's false, because it ignores how writing plays into popularity. Superman is more popular, Batman is more popular - why? Because they've been written as more well-rounded, deeply explored versions of the heroic archetype than female characters because the male-dominated field of comics creators simply aren't skilled at placing themselves in the minds of female characters and giving them equal treatment.
To an extent, again, but comparing Diana to either of them hurts the character, in my opinion; she's never been close to them in popularity, nor has anyone else at DC. Male writers can write as many excellent stories starring, say, Green Lantern, and they'll never make him as big as the others.