Multisite wordpress and subdomain URL collisions

You could just prevent slugs matching existing directories. There are two filters for that.

Example, not tested:

add_filter( 
    'wp_unique_post_slug_is_bad_hierarchical_slug', 
    'prevent_directory_slugs', 
    10, 
    2 
);
add_filter( 
    'wp_unique_post_slug_is_bad_flat_slug', 
    'prevent_directory_slugs', 
    10, 
    2 
);

function prevent_directory_slugs( $bool, $slug )
{
    return is_dir( ABSPATH . "https://wordpress.stackexchange.com/" . $slug );
}