For a long term solution, you would do best to have moodle sit in its own folder and set up a separate url for the moodle site. This would require some dns work and setting up apache or IIS to direct incoming requests to the moodle site. Not knowing how your network/server is set up or if this is hosted or not, it is hard to tell you how to do that but some creative googling will get you there. Then you could just change the link in your new WP site to reflect the location of the moodle site. If you go this route, you will need to update your config.php file and run the replace tool to update the database with the new web address.
A quick fix would be do as you already suggested, just move the moodle folder to the same location in your new WP site. If the new wp site has the same address as your old, it should just work.