We use an atomic orbital in our logo, even though it is scientifically wrong.

Scientists spend a lot of time nit-picking minutiae(1)  but sometimes you have to go with imagery the broad public understands, not try to satisfy that guy at a conference Q&A session who doesn't have a question but just wants to talk about himself.

An atomic orbital doesn't ruin trust in science, the way garbage like the manufactured 'balance of nature' or claiming sugar-free soda causes cancer or denial of agricultural breakthroughs do. What about thinking of small structures as primarily empty space?

Not really. Carl Sagan popularized it, he also popularized really goofy stuff like nuclear winter, but he wasn't inventing things, he was a pop culture communicator. People in science know molecules are packed with stuff. Still, writing in Aeon, Professor Mario Barbatti takes exception to it.

He's right, but I don't get the drama. Barbatti lives in France. If he wants to find anti-science beliefs to debunk, they have replaced England as the leader among rich countries for embracing environmental nonsense over evidence-based thinking, so he could start there.

NOTE: 

(1) If I note a weedkiller doesn't act on a biological pathway found in humans and can't cause cancer a scientist will appear from a bush and declare there is no evidence that it can cause cancer but not impossible, and then bore us all with three 'on the other hand' qualifiers, before then wondering why activists always win culture wars against science.