Part of the process of rigging a character with Uefy Script involves applying armatures to the mesh. Blender does not allow that if the mesh has shapekeys. So this is more of a Blender issue rather than anything the script does. This also means you can get around the problem. Remove the shapekeys from the mesh, rig the mesh with help from Uefy Script. Then copy the shapekeys back to the now rigged mesh from a copy of the original mesh.
I know that Blender has support for this type of data transfer. Seen some stackoverflow articles, you can search for them. But I have not used shapekeys myself, I can not provide instructions.