macOS Sierra 10.12.2 DOD CAC Access Issues
I found this Apple developer forum post that seems to solve my issues:
The workaround in this post disables Apple's CryptoTokenKey PIV support which was conflicting with Centrify's tokend support when using Chrome/Safari vs. Outlook. The former preferred the CTK, the latter tokend. Both cannot be used simultaneously since they require exclusive access to the card. Disabling CTK pivtoken allows Chrome/Safari to fall-back to using Centrify's tokend support.