How to delete Panel variant programmatically
I just had to do this recently. If the variant is exported to code (like in a Feature) this will revert it. Otherwise it will just delete it.

   function MY_MODULE_update_N() {
     ctools_include('export');
     $page = ctools_export_crud_load('page_manager_handlers', 'node_view__test123');
     ctools_export_crud_delete('page_manager_handlers', $page);
   }