You can add an uninstall file that uses WP_UNINSTALL_PLUGIN to remove all database tables the plugin created. Will only happen on deletion of plugin, not on deactivation.
// exit if uninstall/delete not called
if (!defined('ABSPATH') && !defined('WP_UNINSTALL_PLUGIN'))
// otherwise remove custom table
$tablename = $wpdb->prefix . "pmpro_membership_levels";
// setup the query
$sql = "DROP TABLE <code>$tablename</code>";
// execute the query
require_once(ABSPATH . 'wp-admin/includes/upgrade.php');
I think it's pretty safe to assume that if an administrator is deleting a plugin you can wipe the database.