Core tomatoes with a paring knife and cut a larger 2"-wide circle on top of each. Using a small spoon, scoop out insides, then place tomatoes upside-down on a paper towel-lined baking sheet and let drain while you prep the filling.
In a large skillet, heat olive oil over medium-high heat. Add shallot and garlic and sauté until fragrant, 1 to 2 minutes. Add sausage, breaking it up with a wooden spoon, and cook until browned and cooked through, 8 minutes.
Using a slotted spoon, remove sausage mixture to a large paper towel-lined bowl to soak up grease, then discard paper towel and stir in basil, panko, fontina, and Parmesan.
Place tomatoes in a small baking dish and season insides with salt and pepper. Stuff tomatoes with sausage mixture (filling will shrink as you cook, so be sure to mound tops until they look like they’re overflowing).
Bake until cheese is melting and tops are golden,15 to 20 minutes. Let cool 5 to10 minutes and serve with a simple green salad.