Well no one else has offered an answer yet, so I'm going to suggest one approach you could take would be to make /etc/pam.d/common-auth a file rather than a symlink to /etc/pam.d/common-auth-pc. That way pam-config won't change it.
Code:
$ cd /etc/pam.d/
$ unlink common-auth
$ grep -v ^# common-auth-pc > common-auth