I've seen the question several times now about whether ConfigMgr supports setting OpsMgr agents into maintenance mode during software deployment. The answer is mixed. If we take a look at the MOM Maintenance Mode tab for a program we see the options available.
Notice that the text says that setting this option in ConfigMgr will result in any alerts being suppressed for the duration of the program. When you set these options ConfigMgr WILL stop alert generation ON THE AGENT by simply pausing the health service. However, there is nothing done to suppress the alerts that may be seen from the various other components that may be interacting with the agent, such as the health service watcher. We are aware that there needs to be improvement in this area and are anticipating some changes in how this performs so that, when selected, all components will be placed in maintenance mode.