There are some ways to manage this:
1. You may give the users more time before the reboot (maximum30 mins)
2. You may disble installation of updates that require reboot
3. Enable restart later with a 60 minutes delay.
To enact one of these policies go here:
Navigate to policy
Choose “Windows Intune Agent Settings” and click “Create Policy”
Here are the update options:
Now notice the: “Allowed logged on users to Control Windows Intune Restart”
Should be set to YES
In the other boxes you may set the time to max in order to steal minimal of focus with the restart prompt Box.