The impact on deleting or deactivating will be the same, if the user has any scenarios scheduled to run they will fail to run. Deactivating removes the license but keeps the reference to the user, so you can see the user name in the history in the project version control, etc. Deleting the user will just show "deleted user". In general deactivation should be preferred but you should check your license terms to make sure you are not violating them.
