We have this issue in our environment too. Currently I am using Inventory to scan for stopped services and Deploy on a heartbeat schedule to turn those services back on. However, I am starting to play around with the idea of using Group Policy Preference instead. Here is how you can setup Inventory and Deploy to automatically handle this.
Create a dynamic collection to filter for all and create two filters for Services.
Set the first filter for Name and equals to whatever service you want (WSUS in the example, wuauserv)
Set the second filter for State and Does Not Equal "Running"
(If you want to search for Autostart, create another filter for Service - Start Mode - Contains - "Auto". That will find services that are also set to Autostart.)
Create a package to run CMD command for starting a service.
Create a schedule to trigger on heartbeat. Link the target to PDQ Inventory collection and the package to the start service package.