Azure Automatic Provisioning

Is is possible to apply the automatic provisioning at the enterprise level and not the org level. Initially we setup SAML at org level and applied automatic provisioning. Then went and applied SAML SSO at the enterprise, this config cascaded down and applied to all orgs, however in so doing we broke the auto provisioning. No matter what we supplied as tenant url under admin credentials could get it to work? I would really need to find a way to pull someone from all orgs when they are removed from the enterprise. Looking for help please?! Please and thank you

Note we are part of the github campus program on the enterprise cloud if that makes a difference. I read that this may be in beta, but not sure.