What's the best way to stop Greek Fire?
Solution 1:
I finally beat one of these by simply stacking nothing but riflemen everywhere I could, with fully upgraded barricades with archers behind them to pick off the wusses so I could build up the rear barricades. They never got through my first barricade until the Greek Fire showed up, and the 20+ riflemen I had managed to take him down. (Fortunately, the barricades held long enough - he was almost out of range of most of my riflemen!)
For winning this, my first non-story Den Defense, I was rewarded with the Assassin Caltrop Unit and also this little thing called "Greek Fire Barricade" that I'm willing to bet will come in handy later. :)
Solution 2:
Try putting lots and lots of caltrop bombers everywhere and shoot lots of cannon balls at it. While you're at it, try helping by shooting it with your gun.