Options:
You can drop the database. This will work if you want to start with a clean slate every time. You may want to look into kickstart or terraform to set default applications, accounts, and other items up every time. You can load all the users into a tenant (not the default one). Then, when you are done with loading up the users and want to clean up, you can delete the tenant, which will remove all users associated with that tenant. This option maintains all the other non tenant settings (IdPs, emails templates, themes, etc). You can use the bulk delete API. You can start deleting blocks of 5-10k users and increase the number deleted with each API call. This will be slower, but has the benefit of leaving the rest of the system untouched.