For Dynamics 365 deployed on premises, you can disable a user, but online you need to remove the license to disable.
- Reassign records in CRM. Do you want to reassign record ownership for cases, opportunities, accounts, contacts and other entities? If so, deleting a user will not do this automatically so you should update with Advanced Find or another approach.
- Does the user own workflows? If so, new system jobs will fail when you disable or delete the user. This is a good reason to use system accounts that are not subject to change as the owner for these processes.
- Deleting users in Dynamics is not the same as deleting them in Office 365. Some organizations have different administrators for Dynamics and Office 365, so you need to have a process to coordinate these actions.
- Auditing may require you to keep track of who did what to which records. Do not change a user name to misrepresent the actors in past transactions.