YES.
Follow the backup/restore procedure as described in the FAQ.
www.jms2win.com/en/faq/faq-joomla-multi-sites#cat-268
The tips consists in doing the backup with a tar -chzf where "h" means replace the symbolic links by a physical path.
So that, when you will restore the slave site, you will have the PHP code.
Once the backup is restored, you can uninstall JMS that might be present in the slave site and also remove the JMS patches that are present. Becarefull that when you uninstall JMS, this restore the backup of some files (including the configuration.php file that is the one of the master). So keep you slave "configuration.php" to be able restore it after the uninstall of JMS.
To remove the patches, we also recommend that you redo an unzip of the standard Joomla package over the restore site. This will remove all the JMS patches installed in the "core".
Concerning, the DB and the "configuration.php" of the slave, JMS does NOT touch them except if you have decided to share the content of some extensions.
In this case, the DB may content sharing of tables instead of the physical tables.
If this is the case, you will have to export with PHPMyAdmin the physical tables and restore them into you slave DB after that you have changed the table prefix of the physical table to restore.
If the slave DB didn't had any sharing, you don't have to do anything on the DB.