Usually, if authentication is right in place, it's as easy as copy and paste the URL that appears when you click that app in the Accesspoint and put it as a URL for the user. Then, instead of going to AP and clicking the app, he will be direct to the one in the link.
They will log in to their computers right? You can create a Windows shortcut to the app. Or if they work with a corporate intranet portal, you can set the URL there. Or a bookmark in their browsers... There are many options.
But the key thing is how users get authenticated to QlikView, and how QlikView has configured security in the QMC. Is that Active Directory + NTFS, is that a LDAP server + custom login page?
Without knowing in more detail the login flow of the users is very hard to say.
If that is going to be the case, you should build dynamically that button (or more properly, the link within the button object) so you can get the user credentials, for example, and set them open the files they have access to.
However, if you have several users with access to several apps, then I don't see the need to not use Accesspoint: that is what Accesspoint is for.