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
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