List Custom Taxonomy Values according to a Post Meta Value

This will return an array of term objects, if you need these processed to be hierarchical or something, that’s pretty easy, I think the challenge you were having was getting the term objects.

//get posts
$args = array(
    //basic stuff
    'post_status' => 'publish',
    //meta query
    'meta_query' => array(
        array(
            'key'     => 'your_key',
            'value'   => '1'
        )
    )
);
$posts = new WP_Query( $args );

//get categories from posts and amalgamate them
$categories = array();
foreach( $posts as $post ) {
    $new_cats = wp_get_object_terms( $post->ID, 'your-taxonomy-slug' );
    $categories = array_merge(
        $categories,
        array_diff(
            $categories,
            $new_cats
        )
    );
}

I feel like there might be something that you could do with the get_terms hook, but I can’t put my finger on it (shy of querying for every term to see if it has posts that meet the condition, but that’s way less efficient than my method I think).