Bring a large pot of salted water to a boil and cook the whole wheat linguine according to package directions until al dente; reserve about 1/2 cup pasta cooking water, then drain.
Heat the olive oil in a large skillet over medium-low heat. Add the minced garlic and sauté for about 1 minute, until fragrant but not browned.
Add the drained, diced capers, chopped basil, thyme leaves (remove stems), chopped parsley, crushed red pepper flakes, black pepper and salt; sauté for 1 additional minute to release the flavors.
Add the cooked linguine to the skillet along with the baby arugula. Toss to combine, adding a splash of reserved pasta water if needed, and cook just until the arugula wilts and the pasta is heated through.
Remove the skillet from the heat. Gently fold in the halved grape tomatoes, then sprinkle with the freshly grated Parmesan and toss once more to combine.
Serve immediately, adjusting salt and pepper to taste.