Only lets the top level term in the permalink structure

only-top-term-filters.php

<?php
function wpse147453_remove_child_categories_from_permalinks( $permalink, $post, $leavename, $sample ) {

		if ( in_array( $post->post_type, array( 'focus_courses' ) ) ) {
			// Allow for slug to be editable
			$slug = $leavename ? '%' . $post->post_type . '%' : $post->post_name;
			// Generate premalink prefix based on post type
			$prefix = 'courses';
			// add parent term slug
			$term_slug = focus_top_term( $post );
			// Array of custom permalink tabs
			$permalink_tags = array(
				'%prefix%',
				'%term_slug%',
				'%postname%',
			);
			// Array of permalink values
			$permalink_values = array(
				$prefix,
				$term_slug,
				$slug,
			);
			// Generate the permalink
			$permalink = str_replace( $permalink_tags, $permalink_values, '/%prefix%/%term_slug%/%postname%/' );
			$permalink = user_trailingslashit( home_url( $permalink ) );
		}
		return $permalink;
}
add_filter( 'post_type_link', 'wpse147453_remove_child_categories_from_permalinks', 1, 4 );

function focus_top_term( $post ){

	$terms = wp_get_object_terms( $post->ID, 'course_categories' );
	$plucked = wp_list_pluck( $terms, 'parent' );

	// getting parrent term object and it's slug
	$term = get_term_by( 'id', absint( $plucked[0] ), 'course_categories' );
	$slug = wp_list_pluck( array( $term ), 'slug' );

	return $slug[0];

}