*** use at your own risk ***
One way would be to:
cp -af public_html /home/newuser/public_html/userdir
mv userdir userdirbackup
cd /home/newuser/public_html chown -R newuser.newuser userdir (if you run php as a cgi)
cd /home/newuser/public_html chown -R newuser.nobody userdir (if you run php as a module)
Where userdir is the existing site, and newuserdir is the master account where you want the old main site to become an addon.
Then delete the old user from WHM.
Then go into cPanel for newuser and create the addon domain using userdir as the subdirectory.
If something does wrong you can restore the old account from backup OR recreate in in WHM then
mv userdirbackup userdir
if all works well for you once you create the addon domain you can remove the backup from the home directory.
But this method probably brings over a lot of unecesarry files so...