Try something like this (YOUTPOSTTYPE is the name of your post type):
function deactivate () {
$args = array (
'post_type' => 'YOURPOSTTYPE',
'nopaging' => true
);
$query = new WP_Query ($args);
while ($query->have_posts ()) {
$query->the_post ();
$id = get_the_ID ();
wp_delete_post ($id, true);
}
wp_reset_postdata ();
}
It works in my plugin, it should works in your's. (This has been tested with WordPress 3.5.1).