Preheat the oven to 375 degrees. Place the pie shell on a baking sheet and par-bake the pie shell until lightly brown. To par-bake -Thaw crust for 10 minutes, prick the bottom with a fork, and bake for 10 minutes. Remove from the oven and set aside.
In a medium skillet, fry bacon. Remove to a paper towel-lined plate. Set aside and crumble when cooled.
In the same skillet with the bacon grease, cook onions until translucent and slightly caramelized. Remove from the skillet with a slotted spoon and set aside.
Line a baking sheet with a few layers of paper towels. Slice the tomatoes and lay them on the paper towels in a single layer, then sprinkle with the salt to draw out the tomato juices. Let sit for 10-15 minutes, then use fresh paper towels to pat dry the tomatoes and remove most of the juices, so the pie doesn't turn out soggy.
In a small mixing bowl, stir together cheddar cheese, mozzarella cheese, bacon, onion, pepper, mayonnaise, and sour cream.
Assemble the pie: In the pie shell, layer tomato slices, basil, and cheese mixture.
Bake in the 375-degree oven for about 35-40 minutes. Let rest for at least 10 minutes before slicing.