In my testing with the AD provider this shouldn't be a problem. The user is automatically added to the child portal (UserPortal table) when they visit the child site (as long as the authentication has been setup on the child portal). My question is how extensive are your individual department child portals going to be? Are they basically only one page or multiple pages? Who is going to administrate these child portals? You or are you going to assign a user to be the administrator for the individual portal?
If you're only going to be using one page per department then I'd personally just go with an individual page on the parent portal and make it only available to the users in that group. This can be quite easy to do if your users are broken up by department in your AD as you can create the DNN Security Role that matches the AD Group and the users are automatically added to that group when they log in. Let's say I've got the following AD groups (Sales, Marketing, Management, and Customer Support). All that needs to be done is for those DNN roles to be created and Synchronize checked in the AD settings. Then, in the one page per department scenario, as the administrator I can create the following menu items (Sales, Marketing, Management, and Customer Support) and set the View permissions on the page to the corresponding group. Then when the Bob who is in Sales logs in he see the Home page and the Sales page but not the other three, when Joe, who is the Marketing Manager, logs in he sees Home, Marketing, and Management, etc. You could also have multiple pages per department under the parent menu item so it doesn't necessarily have to be a one page per department scenario.
I guess what it really comes down to a couple of things....who's doing the administration on the pages/portals and how much freedom are you giving them? IE: you can setup Page Editors as well and those users can add/remove modules and edit the content on the pages they're an editor of. Ultimately, what's going to work best for you as the overall administrator. If you've got 30 or 40 departments then giving each department a page section on the parent portal is going to make the menu a bear for you as an administrator. If you've got a dozen or so then it shouldn't be too bad.