You have to sign out of Messages/FaceTime on each device unless you are using you are using Apple School Manager. From the article below.
Disable FaceTime and Messages
FaceTime and Messages are off by default; however, another user with the appropriate privileges can enable these features. Depending on your role, you may be able to disable FaceTime and Messages for your institution.
- In Apple School Manager
, click Settings at the bottom of the sidebar, then click Accounts
below Institution Settings. - Click Disable next to FaceTime & Messages.
- Note: Before you disable these features, you may want to warn your users that they won’t be able to use their Managed Apple IDs with these features anymore.
Edit institution settings in Apple School Manager - Apple Support