The Sphere module needs to provide a sphere.install file, with the hook_uninstall function to remove it's variable 'sphere_node_types'
/**
* Implementation of hook_uninstall().
*/
function sphere_uninstall() {
variable_del('sphere_node_types');
}
You can do this for the 5.x-1.x-dev version as well. It's always courteous to make sure your module cleans up after itself.