Preemptible instances should not have any associated auto-scaling. It is common for people to run pre-emptible instances as part of a "Managed Instance Group", with which you can associate some kind of autoscaling policy.
You can run preemptible instances without any kind of management or with only very simple management and you should be okay. I recommend a simple managed group with a policy of, "I want maximum one of these instances running at all times and, if it gets preempted, then please start a new one."
If you're using Google Cloud, don't deny yourself the cost savings of preemptible instances. When I was using the same infrastructure, preemptions were very rare!