Isn't this misinterpreting the results of that experiment? The Geiger-Marsden experiments established that most of the mass in an atom is concentrated within the nucleus, where all positive charge is located. It does not try to establish whether or not the area outside the nucleus is empty or not.

The (oversimplified) notion that the matter we typically deal with is mostly empty space is a direct consequence of that experiment, not an artifact of the Bohr model.