Considering that Three.js seems to have several backends for rendering, it should be possible to make a desktop based Three.js editor using Qt (which has its own JavaScript implementation) and a Qt-specific backend.
I believe Qt Canvas3D[0] is what you're suggesting. If I recall, one of the default project template(s) for this used three.js right out of the box.
Does anyone have any real-world Canvas3D stories? I've no experience with it. Things like potential idiosyncrasies its implementation relative to major browsers seems worrisome. Feature lag also might be a concern, especially with bleeding-edge features found behind flags. Not to mention the horror story that is Web Workers.
Granted, there's usually pain whenever you insist on having your cake and eating it too, it's just a matter of where.