WDQS is by design a fragile service. We allow arbitrary users to run arbitrary SPARQL queries. This is similar to allow any user direct access to our production MySQL databases. This is fine as long as the expectations are managed. It is definitely wrong when services from which we expect stable response time and availability start depending on it.
Splitting WDQS in a public, do whatever you want service and a different more controlled service make sense. This would be similar to what we do with MySQL, splitting it between a production service and labs replicas, with different expectations.
My understanding is that the structured data on commons project will rely on WDQS for some of its functionalities. If we want that project to be stable, we need to address the WDQS stability issues.