I finally figured out the details of how to replace a Centrify Samba 3.6.x package with CentrifyDC-adbindproxy v5.3 and CentOS 6.x supplied Samba4 packages:
Backup your smb.conf file:
cp -p /etc/samba/smb.conf{,.bak}
Uninstall the Centrify Samba package:
rpm -e CentrifyDC-samba
Remove symlinks created for the Centrify Samba package in /etc/samba/:
cd /etc/samba/
unlink lmhosts
unlink smbusers
Install the Samba4 packages supplied by CentOS or RHEL:
yum install samba4 samb4-common samba4-winbind samba4-winbind-clients
Rename the backup copy of your smb.conf to replace the file removed when the CentrifyDC-samba package was uninstalled:
cp /etc/samba/smb.conf.bak /etc/samba/smb.conf
Start the smb and winbind services to re-create other files removed when the CentrifyDC-samba package was uninstalled:
service smb start
service winbind start
Upgrade the previously installed CentrifyDC-adbindproxy package:
rpm -Uhv centrifydc-adbindproxy-5.3.0-rhel4-x86_64.rpm
Run the adbindproxy configuration script:
/usr/share/centrifydc/bin/adbindproxy.pl
Press the Enter key to accept the script defaults, other answers are shown in bold
Please specify the stock samba winbindd listen path(dir) if it is not in [/run/samba/winbindd] : /var/run/samba/winbindd
The following error messages might be encountered, these are features supported in Samba 3.6.x and not relevant in Samba 4.2.x. You can safely ignore them since they will be commented out by the script.
Unknown parameter encountered: "send spnego principal" Ignoring unknown parameter "send spnego principal"
Unknown parameter encountered: "ignore syssetgroups error" Ignoring unknown parameter "ignore syssetgroups error"
Reset the Samba User/Group ID Cache (Centrify Samba may create conflicting mappings) [Y] : N
I chose not to reset any existing UID/GID mappings since this was an upgrade of a Samba server that already had data with assigned UID/GID values. Given that the range of these values did not change in the updated smb.conf file, all the owner/group information should stay the same as before this upgrade.
Set the centrifydc-samba daemon to start on boot in run levels 3,4, and 5
chkconfig --level 345 centrifydc-samba on
Restart the centrifydc-samba service:
service centrifydc-samba restart