This code will force HTTPS in the canonical URL meta tag of a WordPress site in an instance where SSL is not the forced protocol.

functions.php

<?php

add_action( 'after_setup_theme', 'my_theme_setup' );

function my_theme_setup() {
	/* Customize the canonical URL. */
	remove_filter( 'wp_head', 'rel_canonical' );
	add_filter( 'wp_head', 'my_rel_canonical' );
}
 
/**
 * Output rel=canonical for singular queries.
*/
function my_rel_canonical() {
	if ( !is_singular() )
		return;
 
	global $wp_the_query;
	if ( !$id = $wp_the_query->get_queried_object_id() )
		return;
 
	$link = get_permalink( $id );
 
	if ( $page = get_query_var('cpage') )
		$link = get_comments_pagenum_link( $page );
		
	$link = str_replace( 'http://', 'https://', $link );
 
	echo "<link rel='canonical' href='" . esc_url( $link ) . "' />\n";
}