Etherpad has issues when deleting pads with a lot of revisions (total freeze, confirmed with 72,000 revisions). To avoid freeze of your Etherpad instance, you can use a job queue, provided by MyPads, to safely handle the deletion of pads. See details on https://framagit.org/framasoft/Etherpad/ep_mypads/wikis/Use-the-job-queue.