The weakness of any old man and doll is...tanks. What? Why are you looking at me like that? Did you think I was going to say fire? Sure, Mia's fire magic would burn Gepetto to a crisp just like -that-. Really, though, this lacks imagination. You saw Berg and the Grindery? The world of Lunar has plenty of magi-tech machines at it's beck and call, and who better to get her hands on them than Mia? Ergo, Gepetto is flattened under the treats of a crystalline magi-tank.
Whatever works, you know?