I'm not any more privy to the back-end conversation than most anyone else is, but it sounds like what's going on is more nuanced than that. It seems that the idea on the table went beyond using gender neutral language by default: It was to using gender neutral language even when the person's gender was known with certainty, out of concern that occasionally someone's gender might be unacceptable.
While bulldozering across the landscape with a single pronoun like that might be preferable to willfully and specifically misgendering people, trans people could still justifiably interpret it as a deliberate act of erasure. I'm certainly having a hard time seeing it otherwise; I just spent a slightly absurd amount of time staring at my screen trying, unsuccessfully, to figure out a better, or at least less provocative, word than "unacceptable" to use in that last paragraph.
There are still a lot of lacunae in my understanding of this story, but the way things seem to be pointing is that the "community standard" that Monica Cellio was in violation of was an opinion as much as an action: It would seem that Stack Exchange wants to make being inclusive (not just tolerant) of trans people a community standard, and, by asking a lot of probing questions about the finer details of pronoun usage, she indicated that she's not comfortable adopting that standard.
I think I agree with others that, while SE certainly figured out a way to make literally everyone angry, there's probably no way to make everyone happy here. I suppose the easy reaction is to say that Monica Cellio was fired for thoughtcrime. And, given that the guidelines in question had neither been adopted nor violated yet, it's hard to argue with that summary. But, setting aside the unequivocally awful way that SE has been handling this situation thus far, it's also true that the organization does have a right to decide that it wants to be welcoming (which, again, goes beyond merely being tolerant). And if they do that, step one is to make sure that representatives of SE are behaving in a welcoming way. Volunteer or not, moderators are public representatives of SE, and so SE does have a reasonable interest in (and right to) directing their comportment when they're acting as representatives of SE. It might just not be possible to do that without stepping on the toes of moderators who have a problem with genuinely respecting trans people.
And if that's all they had wanted to do, I'd be a lot less bothered about this whole affair. As it stands, I'm left fearing that they've managed to do more harm than good by emboldening the folks who like to toss around terms like "SJW", and giving them some legitimately bad behavior that they can proceed to conflate with more reasonably-executed efforts to foster inclusiveness.