How to delete a variable during uninstall?
The problem is probably here (from the comments):


  The variable gets set during installation when the hook_schema calls a function to iterate through an array to create database columns.


The uninstall process calls drupal_uninstall_schema(), which in turn calls drupal_get_schema_unprocessed(), which invokes hook_schema().

So the variable is being added again during uninstall, presumably at a later point in the process than your hook_uninstall() is invoked and variable_del() has run.