on the @Legendary Techy Blog regarding this same problem with Exchange 2010. There was also a comment that stated this was still a problem with Exchange 2013 CU1.
I uninstalled SCCM Endpoint Protection and the CU2 upgrade was then able to complete. I could find nothing about this problem in any of the release notes. Microsoft must know about this incompatibility in their software but evidently they choose to ignore it.
Nice job MS.