You can use the Active Roles Management Shell to delete a user from Azure.
To delete an Azure AD user with the Management Shell
- 
On the Management Shell interface, run the remove-QADObject cmdlet. 
For more information on deleting a user from Azure using the Management Shell interface, see the Active Roles Management Shell Help.
NOTE: In Synchronized or Federated environment, remove-QADObject removes the user from AD and then gets synchronized to the Azure portal.
