How many people are going to be mad if I start a "Did Aeris get fridged?" debate?
I would argue that no, she didn't, because while her death DOES motivate the male protagonist, that's not really its primary purpose. If we wanna go all Joseph Campbell, she's the Christ figure in the story; she has to die so that she can redeem mankind and save the world (and she does the latter but the nice thing about FF7 in its original context without sequels or prequels is that we're left to wonder if she accomplished the former). She's the only character who really knows what the fuck is going on, she's the only one who can stop it, and characters like that tend to die.
Of course, there's still the point that she's one of only two major female characters in the game (and, what, five female characters who are relevant to the story in any way? And you could take Yuffie, Elmira, Scarlett, and Elena out with pretty minimal effect on the story), in a series, genre, and medium that's already kind of a sausagefest. It bears noting that the stated purpose of the original WiR list was to point out that if you keep killing off all the likeable female characters you're going to have trouble attracting a female audience.
Course, since then 10 and 12 have done a pretty good job as female-led games -- though both of them had to have whiny blond teenage male POV characters to obscure the point that the most important character in the story was a woman. 10-2 managed an all-female principal cast, though its mechanics revolved around changing into different clothes.
6 of course had two prominent female characters, and insofar as you can say the game HAS a main character it's definitely one of the two of them, but they were still in a mostly-male cast and subject to their own sets of less-than-progressive tropes.
Can't say much about 13 as I never played it, but so far as I know it's got a female lead, at any rate.