One further workaround, though still not perfect, is to initially load a static cover image in the place of the JSmol object. The JSmol 3D chemical structure is only loaded and displayed on mouse-clicking this image.
See e.g. http://chemapps.stolaf.edu/jmol/jsmol/cover.htm
Also, has the advantage that the containing Moodle page is rendered more quickly, even on systems with relatively limited hardware/bandwidth, such as iPhones.
As long as the image is not mouse-clicked, the docking and glossary auto-linking functions are fine. Once, the cover image is clicked, and the JSmol object loaded,they no longer work, though the original situation can be restored through a simple page reload.
Still, would be nicer to eliminate the JavaScript conflicts.