The dialog prompt has to be shown and approved by the user. That has to be done through Javascript, and it can't be done through PHP directly. Our PHP code creates the Javascript which does the request dialog. There are ways to redirect to a full Facebook page with the authentication prompt (not in a pop-up), but it takes the user away from your site and out of whatever they're doing. It's possible through PHP, but I don't think it's what you're looking for.
There are ways to 'ask' Facebook through Javascript if certain permissions are granted, and if not, to ask for them. I don't know them off hand tough. Additionally, it sounds like you're doing all your logic for assigning points through PHP, which means the permission already has to have been granted. You'll need to either move to an AJAX method which can check for permission, request it, and then do a call to your server to assign the points (or whatever you're doing), or do it through PHP with a full-page redirect for permissions with a return value of your page to assign the points and clean up what needs to be done on your site.
Hope that helps,
Alex