It looks like in my version of Symbiosis the only references to the webmail directory in the Apache2 configuration are in /etc/apache2/conf-enabled/symbiosis-webmail.conf and /etc/apache2/conf.d/symbiosis-webmail.conf in lines that look like this:
Alias /webmail /var/www/webmail
So I'm guessing if you comment out those lines that will disable any links from mydomain.com/webmail to the webmail installation. Then I would go to my designated domain and just make a symlink from htdocs to /var/www/webmail
ln -s /var/www/webmail /srv/mydomain.com/public/htdocs
Fingers crossed Symbiosis will not think you are doing something too strange and do the rest for you.
EDIT: I've assumed you're using Symbiosis but shout if that's wrong.