The solution may depend on the backup system you are using. For instance for Veeam Backup and Replication we have a special Management Pack with set of overrides which hide unwanted alerts and objects, this MP also collects events into SCOM which then could be used for further automation.
If your Backup solution produces events which can be collected by SCOM, then you should be able to create a monitor which can change its state when backup is running (backup started - unhealthy event, backup finished - healthy event), this monitor can have a recovery action which runs a PowerShell script which either disables CPU usage monitor for pre-configured group of VMs or enables it.
Of course such a script could be scheduled, but this is not as flexible as monitor tracking backup start-finish events.
We'll investigate if we can create some kind of example for you.
Also I'm not sure how ticketing system is configured in your environment, but maybe it is possible to block forwarding of certain alerts for a specific time, for instance you can specify a schedule for notifications in SCOM.