A couple of improvements:

1. The document says:

email notifications will continue to be sent to the user — If this is a problem, you can change the user's email address in JIRA to an imaginary address, e.g. user@example.com.

email notifications will only be sent to users with browse permission over the project/issue that is generating the notification. In most of the cases, that means that by removing the user form all the groups, they will stop receiving notifications.

On the other hand, filter subscription continue to be sent unless the email is changed.

2. The warning note says:

Before you deactivate a user, you should reassign any issues assigned to that user. You'll need the 'Assign Issue' permission to change the assignee for the issues.

We should add another point saying that they should check that the user is not the default assigneee for a project. If the default assignee of a project does not have 'assignable' project permissions, it can create certain problems within Jira.