This a draft, untested

extending_wp_scripts_class.php

class Alter_WP_Scripts extends WP_Scripts{
    //also $deps method!
    function do_item( $handle, $group = false ){       
    	if( 'handle_here' == $handle ){
    		$handle = false;
    	}
        return parent::do_item( $handle, $group );    	
    }
}
if( !is_admin() ){
	add_action( 'wp_loaded', function() {
	    $GLOBALS['wp_scripts'] = new Alter_WP_Scripts;
	});
}