If you want to run a certain application or configuration that stops either WMI or the Agent Host you have to run it as a "Run Command Line" step. All "Install Software" steps is executed by the execmgr by the Agent Host, and when the application stops either WMI or the Agent Host service it will release the newly spawned process causing the TS to return it as a failure. The workaround is to simply use the "Run Command Line" step when using command lines/applications that reset any of these services. This works since the "Run Command Line" steps are executed by the TS engine which is not dependant on either WMI or the Agent Host service.

The following picture shows a task to install a new ConfigMgr site, a task that resets both WMI and other underlying services, this will work since it is a "Run Command Line" step, if it was a "Install Software" step, it would fail when the ConfigMgr installation would stop the WMI service. The error for this can be seen in the SMSTS.LOG which specifies that the Agent Service is not running. So any task that stops a service that is depending on WMI has to be using a command line step in the task sequence in order to be installed. This type of applications are often anti-virus, VPN, firewalls etc etc.