Hi,
In general it is safe to rename or remove an Organizational Unit (OU), you should always double check what the OU contains first before doing any change.
You should first move the Department A and Department B OUs to their new place, then remove the Workstation OU.
One thing that this may affect are Group Policies (GPOs), you should double check the GPOs to check how they are applied and if these OU changes will affect the GPOs.
Best regards,
Leon