Software for visualization of 3D models of chemical structures with atomic orbitals
As porphyrin mentions in the comments, have a look at Jmol.



It indeed does the rendering as in your original version, but with the many options (see this mo command documentation) and particularly interactivity provided by the scripting, I think you may pedagogically achieve what you are looking for. Proteopedia is a nice website where the efficiently use Jmol's scripting feature for educational purposes (try the green links).