*Also next time use "edit post", then you don't need to post again just to correct yourself.
In redhat, if you change any values in the /etc/pam.d/authconfig file, and run authconfig command, the changes get overwritten.
Please be more specific: what changes?
There's two ways I can think of. I *always* keep config files in a versioning system. That way I can diff & patch if necessary. Isn't "elegant" though and it requires manual intervention. Second way *could be* to use inclusion in system-auth the same way it is used in other services. Say you want to handle passwds yourself and change the system-auth line to read
password sufficient pam_stack.so service=system-auth-password
Then fille new file /etc/pam.d/system-auth-password with this:
password sufficient /lib/security/pam_unix.so nullok use_authtok md5 shadow
save and chattr it. Haven't tried it, but it sounds like it could work. If you have a go at it, please report back if it works.