I think with an empty track the ferrari is faster.
Notice that whenever Alonso catches up to button, it's like he has to brake earlier, almost as if button was part of the traffice, this kind of thing takes away from a potentially fast lap time.
The parabolica also slowed alonso up. He settled far enough from Button's dirty air to make sure he kept the car on track.
I was not surprised he got Button as soon as the track was clear.