Thank you for your post. There is not an option to postpone reboots when there are applications running. Having applications running but no user actively logged on the machine, according to Windows, still means that there is an inactive session. When reboots are needed for patch deployment, our reboot engine will just query the OS for active sessions and we rely on Microsoft for an answer back as to the state of active sessions.
Agents unfortunately don't support custom actions, therefore having custom scripts as part of deployments can't be included for agents. We would certainly encourage you to submit a feature request to see if we can change this for the future. How To: Submit a Feature Request