Microsoft Windows Malicious Software Removal Tool allow a quick check for the most common malware on you computer. Windows-KB890830-VX.XX.exe release an updated version of this tool on the second Tuesday of each month. Microsoft Safety Scanner an updated tool that expires 10 days after downloading.

Both executables have same parameter to run it on silent mode:

name-executable.exe /Q

So to execute Microsoft Safety Scanner (as example)  within OCS:

Create a new Package and execute msert-x86.bat with those contents:

msert-x86.exe /Q

Upload as zip, activate, and assign a computer to run it. When execute on the client machine it could fail and give an exit_code

• EXIT_CODE_6 At least one infection detected. No errors.
• EXIT_CODE_7 At least one infection was detected, but errors were encountered.
• EXIT_CODE_10 At least one infection was detected and removed, but a restart is required for complete removal

You can see more exit codes on KB891716 but if you want a more detail you can check %windir%\debug\mrt.log

This software does not create a new entry on the Add/Remove Program list. But I will add and entry on the registry under

HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\RemovalTools\MRT\Version . So to add it on OCS you need to create a registry entry

Registry -> New Data

Name (you choose): MRTVersion

Registry hive:  HKEY_LOCAL_MACHINE

Path of the key: SOFTWARE\Microsoft\RemovalTools\MRT

Name of the key that will be read: Version

You will get a string:  A769BB72-28FC-43C7-BA14-2E44725FED20 (This one is for January 2013)