Heat a medium saute pan over medium-high heat. Add the oil, then the turkey sausage, and cook, breaking up the sausage into small pieces with a wooden spoon, until it is beginning to brown and fully cooked, about 5 minutes. Add the shallots and garlic and continue to cook until the sausage has browned and the shallots are soft, about 4 minutes. Set aside to cool.
Bring a large pot of salted water to a boil. In a large bowl, using a rubber spatula, mix together the cheeses, tomatoes, basil, chives, salt and pepper. Fold in the cooled sausage mixture. Cover and refrigerate until ready to use.
Cook the pasta to al dente according to the package instructions. Strain the pasta well and spread it on paper towels in one layer to dry completely.
In a medium saucepan, heat the oil over medium heat to 350 degrees F. In small batches, fry the dried shells until golden brown and crispy, stirring occasionally so they don't stick to one another. Remove the shells with a slotted spoon and drain on a paper towel-lined plate. Continue with the remaining pasta.
Fill each shell with about 1 teaspoon of the filling.