When we were there in 2004 everybody was talking about Yesil Ev (yellow house) as the best of the Ottoman Inns at that time. Friends of ours had a meal there (they were staying at the Four Seasons), and enjoyed it very much. We walked by it and it seemed very nice. Location could not be better, although I don't know about rooftop views.

Note that if you stay in this area, there's a great little bazaar which is just a street full of shops, but is kind of like a mini-grand bazaar. It's call the Arrasta Bazaar, and is just behind the Blue Mosque. I had great fun there.