Stopping a service won't throw an error even if the service isn't found. However, if you try to start a service and it isn't found, then wyUpdate will rollback the update and show the error. The reason wyUpdate shows an error if the service can't be started is that it's implied the service is required by your app -- thus a failure to start a service is a failure to update your app.
If you want conditionally start services after your update then you can do it by executing a *.bat file. This way you can either choose to start a service or not based on the company (or however you're handling it). You can still stop the service using the Update Action within wyBuild -- it won't throw an error if the service doesn't exist.
Tell me if this helps.