A quick update on the problem. After re-running ispconfig3 update.php email was still not functioning. It turned out that the CentOS yum update I did updated postfix, which removed the postfix built during the perfect server setup and replaced it with the repository postfix that doesn't seem to have mysql compiled in.
yum remove postfix, then rpm -ivh on the postfix rpm built during install, then re-run the ispconfig3 update.php and finally email is back.
If you're like me and regularly update the os using yum, I suspect the thing to do is to always exclude postfix from yum updates in the future,