Preheat oven to 400°F. Put eggplant on a rimmed baking sheet in a single layer. Add 2 Tbsp olive oil and stir to coat well. Season with black pepper. Bake for 20 to 25 minutes, until tender and lightly browned, stirring once or twice. Remove from oven and set aside.
Meanwhile, cook the linguine according to package directions. Drain coat with about 1 Tbsp olive oil and set aside.
Brown and break apart sausage in a large skillet. Drain. Set aside.
Coat the skillet with 1 Tbsp olive oil and heat on medium high heat. Add onion and cook until translucent, return sausage to skillet stirring to mix. Add oregano, red pepper flakes, and garlic and cook for 1 more minute.
Add tomatoes and bring to a simmer, then reduce heat to medium. Stir in eggplant, raisins, and capers and simmer until thickened slightly, 5 to 7 minutes. Stir in vinegar and all but 1 Tbsp cilantro. Season with salt and pepper to taste.
Return linguine to the pot it was cooked in and put on low heat. Immediately add eggplant-sausage mixture and mix well. Divide among 4 plates and top each with 2 Tbsp cheese. Sprinkle evenly with remaining cilantro.