I didn't notice anything requiring that window blinds must be closed though; it doesn't really seem to me that it would be too hard to just look out the window and figure it out.
For example: http://www.af.mil/news/story.asp?id=123149266
It would be pretty easy to slip a gps antenna behind the shade before you closed it as well.
Passengers, beyond curiosity, have very little use for GPS during a flight. When I'm on a plane I could really care less what my location is. I'm more concerned with how much longer I have to wait before arriving at my destination.
The parts of the security directive that bother me most are the restrictions on access to carry-on belongings and items on your lap and not being able to get up from the seat.