There was still a female character on the show, she just wasn't human like you mentioned. And Fred, though incredibly smart, would never have survived that final battle. Heck, Gunn and Wesley didn't either (from my poor recollection of the After comic, heck Wes was dying in the final shot). This was too much of a stretch for the article. There was only one other female character on the show, and both the character and the actress was poorly handled in the end, no question, but I'm just not buying this 'Whedon's anti legacy against female characters' bandwagon that a lot of click bait articles want to run with.
I don't think this article is an indictment on Joss Whedon, although I will say based on this thread that what happened to Charisma Carpenter specifically doesn't shed a positive light on him.
Like the wider point it is making is that the female characters on the show are essentially disposed of once the "nurture" aspect is seemingly played out (the article says this is about pregnancy which I agree is a weak analogy) but I think the point stands. Cordelia was 100% the "mother" of the group, which is a role that Fred filled to an extent when they wrote Cordelia out. The second Illyria takes over Fred, the show completely loses that vibe in the group dynamic because it just becomes a show about a bunch of angry/ depressed dudes and this ancient god trapped in the guise of their companion playing with their emotions. Don't get me wrong, I love Illyria and will say I like what they did with Fred's character (coming through Illyria and such, humanising it). I love Illyria's effect on the group and the group dynamic. But it came at the cost of any female energy in the core cast on the show, which IMO was to its detriment. It's not to say that Joss or the other showrunners set out to be misogynistic, it's just an acknowledgement that the female characters of the series were done dirty and I personally think they all were. Including Darla.
Illyria could have gone into Gunn or some shit, at least that would have given the dude an actual plot. If we stop to think about "why was it Fred" the answer is not exclusive to but definitely
includes the fact that she is female. Which, again, would have been less of an issue with Cordy still in the mix. And I will say that I think the Illyria storyline was more impactful
because it was Fred - if it had been another character it might not be so interesting but we'll never know.
Gunn was dying and Wes was dead already. If the show had been renewed for another season Amy Acker would still be a regular and we would almost certainly see more Fred, but since it didn't, all these characters (aside from Lorne and Conner) met a violent end at some point.
It's not really about how much Fred we see as much as it is about the choice that was made to replace her character. I do think that a season 6 could have helped (I remember reading that they were going to bring Fred back more through Illyria in Season 6, I imagine it would have been a plotline about how you can't actually erase a human soul/ consciousness).
I have a particular thing about Fred vs. Illyria because the first time I watched the show through I was so deeply depressed and engrossed that I broke down during that episode and then
didn't even realise that Amy Acker was still on the show until fake!Fred popped back up again a couple of eps later (I know, it's mad - I must have been fast forwarding through the opening credits).
My tl;dr is that I think the Illyria storyline was fab but I agree with the wider point the article makes about all the female energy being sucked out of the show. I think it's a mild stretch to say that "they all got pregnant then were disposed of" but I can see where that viewpoint is coming from for sure because that's kinda what happened?