Yeah, we had federated accounts at one of my previous companies. I know that you can set it up to be integrated with your SSO providers and that they can create federated accounts with predefined settings/permissions. From what I recall though, I think you can still manually make non-federated accounts in the admin console.
The only way I can think of to restrict that is to limit who you give admin permissions to modify accounts. If you limit it to just 1 or 2 people (maybe even just your system admin), then no one else will have the option to manually make non-federated accounts. Then it just comes down to, like Jen said, create internal processes to say how new accounts will be set up.