http://www.youtube.com/watch?v=vzrfX96PVEU
--- promoted to front page by Ian ---
Believe it or not, this is something the developers tried to prevent from happening (that's why you can't air assassinate Francesco or kill him from a haystack, because then he would be dead right away). To do this hire the nearby group of courtesans before you climb up the large building after Francesco. Place them by the cart of hay right by where he will appear when you chase after him. Then go to Francesco to start the scene. Luckily this isn't one of the scenes that will cause your hired group to disappear. When you chase after him the group will block his way, which can give you an opportunity to kill him right when you get out of the haystack. This seems to be just a little faster than throwing knives at him.