Currently, that is the behavior of the Shavlik Scheduler and there is not way to change this behavior.
Our Protect 9.2 release due out late Summer will change this behavior to not run if the scheduled scan/deployment or deployment time is missed.
As of now, the Scans - Deployments run through the agent are the only way to prevent the jobs to run if the scheduled time is missed. This can be setup in the Agent Policy. But this would require to switch over to agents.
Let me know if you have any questions,
Thanks Charles. I guess I'll wait for the next version, 9.2.