The Malicious Software Removal Tool (MSRT) can be prevented from being offered as an update through Windows update.
Windows Registry Editor Version 5.00 [HKEY_LOCAL_MACHINE\SOFTWARE\Policies\Microsoft\MRT] "DontOfferThroughWUAU"=dword:00000001
Windows Registry Editor Version 5.00 [HKEY_LOCAL_MACHINE\SOFTWARE\Policies\Microsoft\MRT] "DontOfferThroughWUAU"=-