Where does one set such an option?
In /etc/pam.d/<service_name> (where <service_name> is the name of the service that you want to apply the option to.
For example, if you're working with sshd, the file /etc/pam.d/sshd contains (amongst other things) this like that tells it to lookup accounts in Open Directory:
auth required pam_opendirectory.so try_first_pass
If you want this lookup to ignore the home directory then add 'no_check_home' to the options:
auth required pam_opendirectory.so try_first_pass no_check_home
However, there's no way to do this on a per-user basis - it'll either check all user's home directories or no users'.
I still cannot recommend doing this, though. I'm still at a complete loss to see what problem it is you're trying to solve here. The home directory issue doesn't prevent your admins from logging in.