Hi chrisrein,
The most ideal method would be performing a clean install with Centrify agent 5.3.3 while first un-install the previous version of Centrify agent 5.2.4. As Centrify always recommend customer should upgrade the Centrify client FIRST; then the operating system.
However, since you are already on OS X 10.12 Sierra. Simply performing an upgrade by running install.sh on the existing agent (From 5.2.4 to 5.3.3) should work just fine as well.
Hope this can answer your query. Thank you!
Ivan