One method could be, to use a script to apply an override MP, instead of applying maintenance mode.
By setting a scheduled task to import an MP, containing a single override for Veeam VM CPU Monitor, then you can have granular control over that single monitor without disabling the whole VM object.
However, importing override MP will take longer to take effect than setting maintenance mode.
The MP must be imported in SCOM Management Server, then delivered to all relevant agents, then loaded by the agent, causing additional network traffic, agent cpu usage, and overall additional load on SCOM. The same applies in reverse when running another Task to delete the Override MP.
However since Microsoft do not have the feature of scheduled overrides, above is the only method to achieve your aims.
Hope that helps,
Vice President, Product Management