If user is authenticated by the domain, users will have access to the Accesspoint as it´s only a "site".
The only thing that you can configure inside QlikView is access to QlikView documents.
So you need to configure access restrictions to Accesspoint outside QlikView.
For example host Accesspoint inside a portal and customize authentication.
If you set QlikView server to use DMS instead of NTFS, prohibit user when on Accesspoint, to see any documents, but either way they will not be able to open documents if they don´t have proper access rights configured in QlikView.