The simulation in Factorio isn't "harmful", it's just incomplete (in a way the author of the post doesn't like) because the implementation has started from the factory, not from the world (like Minecraft or Dwarf Fortress did).
Imagine someone wrote a blog about how Space Invaders encouraged militarism and xenophobia. It sounds like a parody, but then so does this blog post.
https://www.youtube.com/watch?v=p--dHQIeagE
It's super cute, and also hits like a truck. Detroit techno is a really inspired musical choice for this kind of thing.
This sounds plausible, but I'm not sure if it's entirely true: the factory building is explicitly set in a foreign world and not in our on as any of the many many other factory sims out there.
I think it is more like the authors had the "fight against xenos with factory" idea as a start and then got severely detoured into the factory building after they had the basics of the world done.
When developers want to pass a message they use catmen from the Avatar movie. Imagine changing alien models to that. There will be another whole layer of questions.