With the latest release of System Center Configuration Manager (SCCM) Current Branch (build 1806), you can now exclude organizational units from the Active Directory System Discovery.
To configure such exclusion(s), go to the Administration workspace of your SCCM console and reach out the Hierarchy Configuration\Discovery Methods to edit the Active Directory System Discovery
Then edit your Active Directory containers settings from the General tab; you will then be able to define the exclusion within the Search Options section
