Is it safe to include a javascript file in a template’s php file?

As @N00b mentioned Yes, it is safe adding a JS script as long as it doesn’t include any sensitive information. JS is fully exposed to client, you shouldn’t do it anyway.

But your situtaion it is better to create a site specific custom plugin and add JS using it.

Example :

function themeslug_enqueue_style() {
    wp_enqueue_style( 'core', 'style.css', false ); 
}

function themeslug_enqueue_script() {
    wp_enqueue_script( 'my-js', 'filename.js', false );
}

add_action( 'wp_enqueue_scripts', 'themeslug_enqueue_style' );
add_action( 'wp_enqueue_scripts', 'themeslug_enqueue_script' );

More Details : Plugin API/Action Reference/wp enqueue scripts