In a large non-stick skillet, heat olive oil over medium heat until shimmering. Add the parsley, basil, and thyme. Cook for about 5 minutes or until the herbs are crisp. Remove and discard the herbs using a slotted spoon.
Add the shallots to the olive oil and sauté for a few minutes until tender. Add the garlic and sauté for 1-2 minutes, or until fragrant but not browned. Add the crushed tomatoes, red pepper flakes, and black pepper. Bring to a simmer, reduce the heat to low and cook until the tomatoes break down and the sauce thickens, about 25 minutes.
While the sauce is cooking, prepare the pasta according to package directions. Drain and set aside until needed.
Add the kale to the Pomodoro sauce and cook, stirring occasionally, until wilted, about 5 minutes. Add the drained pasta and cook until heated through. Season with salt and pepper. Spoon into bowls and garnish with fresh torn basil leaves and grated Parmesan.