Plugin API: WP_Rewrite, implementation help needed

I posted about this before, but didn’t get anywhere (going on a month since). I cannot seem to be able to add to, modify or remove permalinks via the plugin API (specifically, WP_Rewrite).

Here is an extreme example, for the purpose of illustration, which I’ve placed in my active theme’s functions.php file (doesn’t work as a plugin either):

function customize_permalinks($rules)
{
return array();
}

add_filter('rewrite_rules_array', 'customize_permalinks');

That should remove all permalinks, correct? Well, it doesn’t, a print_r() of $wp_rewrite->rules shows that they are all still there, and they all still work.

What’s wrong?