That's not necessarily saying people shouldn't be trans. The charitable reading [aside below] is that it could be saying that if they're trans, they should still expect to be disrespected and we should be fine with that.
I think that there are respectful ways to make that point. What are the exact limits to how much respect we should be expected to extend to people who defy our preconceptions of society? The line exists somewhere. But that kind of conversation should be approached with care and clarity. To just hint at that point doesn't imply a nuanced view, but implies a general disrespect to a lot of the hard-won acceptance of LGBT people.
Aside: I don't think I'm wrong calling it a charitable reading. Charity doesn't mean I'm going to think endlessly until I find a non-offensive thing it could mean; I'm still going to weight my reading by how I expect most people to have read it. Ultimately I'm publicly arguing against what other people are reading, not the intention that exists privately in the writer's mind. Even if the author just happened to think now was a good time to remind people they should avoid Ruby vs Python holy wars, it's little use for me to read it as that and respond to that if no one else is reading it that way. If people really think the critics' reading (that the critics have explained) is so off-base, there's been plenty of time by now for them and others to elaborate on whatever the intended reading really was.
You are obscuring the details of the case to make your case and you should be ashamed.
> It's incredible that pronouns can bring down an entire community.
This is obviously talking about the pronouns that transgender folks identify as. Where is the disconnect?
Disclaimer: I don't have a strong opinion about the specifics of the stackexchange case. Without knowing all of the details, it seems the actions and new policy was a bit extreme and will do more harm than good.