This seems problematic because it implies that humans would be perfectly fine with accepting grue over blue if they didn't know about the nature of light.

Right, they would, if for weird historical reasons they also thought of "grue" and "bleen" as reasonable linguistic primitives. So the human scientists would be surprised when the next emerald turned out to be bleen rather than grue, and they'd be able to observe that the shift happened at time T, and thus observe that green is a natural property. So this isn't really much of a problem.