Monitoring of Disabled Application Pools and Websites

So we have a SCOM 2012 SP1 environment monitoring an IIS server that's Server 2012.  The IIS server has all of the App Pools that are not in use disabled as well the Default website is also disabled.  SCOM unfortunately still picks up that these are unavailable and complains ad nauseum.  

So the real quest is, is the disabled state going to be picked up eventually? (Now two days later the server objects themselves are Healthy, so I assume I can just close the alerts but ...)