Toss the Fontina and Gruyere cheese with the cornstarch in a medium bowl to coat. Saute the pancetta in a heavy large saucepan over medium heat until crisp and golden, about 8 minutes. Using a slotted spoon, transfer the pancetta to a plate. Pour off any excess oil. Pour the wine into the same saucepan and bring to a boil. Decrease the heat to medium. Whisk 1 handful of the cheese mixture into the wine until it is almost melted. Repeat with the remaining cheese mixture in about 4 more batches. Continue whisking until the cheese is completely melted and the fondue bubbles, about 1 minute. Stir in all but 2 tablespoons of the pancetta. Season the fondue with pepper, to taste.
Transfer the cheese mixture to a fondue pot. Sprinkle with the remaining pancetta and chives. Set the pot over a candle or a canned heat burner. Serve with focaccia and vegetables.