I suppose that you installed it correctly as a must-use WP plugin.
PHP file should be readable/executable by your web server. It’s content should start from <?php tag. Check if user does not have a ‘manage_network_plugins’ capability.

I tested exactly this code at my test WordPress multisite, where it works as expected – URE menu items does not appear under WP Network Admin.

Other workaround – you may replace ‘manage_network_users’ at line #239 of includes/classes/ure-lib.php to some other critical network capability, like ‘manage_network_plugins’.