Best way to areaportal this kind of setup

Either you can put a world brush over the door way, or you can't area portal it, however, you can use a hint brush there quite easily.

yeah hint planes should do it as long as the visible walls have a nodraw on atleast 1 side.

if you're having trouble lining the hints up then 100% Nodraws should work too as long as you don't need to be able to launch projectiles through those points. Using more areaportals in direct contact with each other will only lead to "brush XXXXX touches > 2 areas" warnings and reduced optimizing

For your current situation, from what you have asked for, I would say that extending to the roof would be a better option, mostly because it just seems smoother of a way to handle it. Usage of an areaportal like the second way would defeat the purpose of the areaportal below, if I remember how the source engine handles areaportals on the same plane (renders the bounding box of the areas)

Well, if you want it to be Sky-Open just do a Skybox brush there.
The skybox brush is quite a flexible tool if you get to experiment with it a bit.

http://forums.tf2maps.net/showthread.php?t=13717 this helped me figure out my problem (which was cutting a giant ass roof with a skybox texture while making it visible in both zones)