I think there's a reasonable case that, from a health perspective, many people should eat less meat. But "less meat" !== "no meat".
Elizabeth was pretty clear on her take being:
Most people’s optimal diet includes small amounts of animal products, but people eat sub-optimally for lots of reasons and that’s their right.
i.e. yes, the optimal diet is small amounts of meat (which is less than most people eat, but more than vegans eat).
The article notes:
It’s true that I am paying more attention to veganism than I am to, say, the trad carnivore idiots, even though I think that diet is worse. But veganism is where the people are, both near me and in the US as a whole. Dietary change is so synonymous with animal protection within Effective Altruism that the EAForum tag is a wholly-owned subsidiary of the animal suffering tag. At a young-EA-organizer conference I mentored at last year, something like half of attendees were vegan, and only a handful had no animal-protecting diet considerations. If keto gets anywhere near this kind of numbers I assure you I will say something.
The argument isn’t about that at all, and I think most people would agree that nutrition is important.
It sounds like you're misreading the point of the article.
The entire point of this article is that there are vegan EA leaders who downplay or dismiss the idea that veganism requires extra attention and effort. It doesn't at all say "there are some tradeoffs, therefore don't be vegan." (it goes out of the way to say almost the opposite)
Whether costs are worth discussing doesn't depend on how large one cost is vs the other – it depends on whether the health costs are large enough to hurt people, destroy trust, and (from an animal welfare perspective), whether the human health costs directly cause more animal suffering via causing ~30% of vegans to relapse.
Another angle on this (I think this is implied by the OP but didn't quite state outright?)
All the community-norm posts are an input into effective altruism. The gritty technical posts are an output. If you sit around having really good community norms, but you never push forward the frontier of human knowledge relevant to optimizing the world, I think you're not really succeeding at effective altruism.
It is possible that frontier-of-human-knowledge posts should be paid for with money rather than karma, since karma just isn't well suited for rewarding it. But, yeah it seems like it distorts the onboarding experience of what people learn to do on the forum.
TL;DR;BNOB
("but not obviously bad")