How to add if lt IE9 conditional scripts to functions.php

Yes, that looks broadly correct (barring a missing '). That isn’t a jQuery $, so shouldn’t cause any problems – the dollar prefix here is the usual convention for PHP variable names and won’t make it into the included script.

Or if I’ve misunderstood and you meant your ie.js script assumes jQuery is $ then you can solve that by wrapping it in a self-executing function which defines a scope where $ = jQuery, e.g.

(function($){
    ...
})(jQuery);

Also as of 4.2 there’s a helper function wp_script_add_data so you can write instead:

wp_register_script( 'ie_js', '/js/ie.js',  array(),  '' );
wp_script_add_data( 'ie_js', 'conditional', 'lt IE 9' );