Previously I’ve blogged here, here and here about SCVMM and SCOM maintenance mode integration. In the past if you put Hyper-V hosts in maintenance mode in SCVMM the corresponding SCVMM object for the host is also put in maintenance mode. The problem with this scenario is that you can get some alerts if you patch the hosts automatically or bring them completely down for other maintenance tasks. Now with System Center 2012 R2 this is no longer the case. If you put the hyper-v hosts in SCVMM in maintenance mode:
The computer object of the host is put in maintenance mode in SCOM:
Now you can perform maintenance task on host without getting noisy alerts and we are closer to better automation.
I would like to thanks the VMM product group for listening on my feedback and for those who voted for this feature change.
Cloud Administrator in Azure World 
In SCVMM 2012 R2 and OpsMgr 2012 R2, I can confirm that the computer object is placed into maintenance mode in OpsMgr, however, I still get alerted that the server is down. For some reason, it’s still not getting all objects for the server into maintenance mode.
I’d say forget the maintenance mode integration. Just put the server into maintenance mode from both consoles – OpsMgr and SCVMM
The health service and the health service watcher are the objects that are not put in maintenance mode and they raise alerts but they will be automatically resolved once the server is up again. I think this a good way as you still have some alerts to know what is going on but they will be resolved once the server is up again automatically.
The issue with the health service has been fixed with UR4: http://support.microsoft.com/kb/2992024
I wouldn’t call it an issue as the two alerts will close themselves automatically when server is up but as long as this new state works for everyone it is ok 🙂