Preheat oven to 425°F. Coat 2 baking sheets with cooking spray.
Standing eggplants on end, remove a thin slice of skin from two opposite sides and discard. Cut eggplants lengthwise into 1/3-inch-thick slices. Brush both sides of the slices with 2 teaspoons oil and arrange in a single layer on the baking sheets. Cut tomatoes in half lengthwise and remove seeds. Place them, cut-side down, in the remaining space on the baking sheets.
Bake the vegetables for 10 minutes. Turn eggplant slices over and bake until the eggplant is lightly browned and tender and the tomato skins are blistered, 10 to 15 minutes longer.
Meanwhile, bring water to a boil in a medium saucepan. Stir in couscous, thyme, salt and 1 teaspoon oil. Remove from the heat, cover and let stand until the water is absorbed, 5 minutes. Uncover and let cool for 15 minutes. Stir in the feta, mint and pepper with a fork.
Coat a 9-by-13-inch baking dish with cooking spray. Put some of the couscous mixture in the center of each eggplant slice. Roll up the eggplant slices firmly around the filling and place, seam-side down, in the prepared dish. Cover with foil; bake for 15 minutes.
Meanwhile, peel the skin away from the roasted tomatoes and put them in a small saucepan. Mash with a fork and add the remaining 1 teaspoon oil, salt and pepper. Heat gently over low heat. To serve, spoon the tomato sauce over the eggplant rolls and sprinkle with the remaining 2 tablespoons feta cheese.