Preheat oven to 400°F. Toss eggplant in 2 tablespoons of olive oil and season with salt. Transfer eggplant to a large roasting pan and roast for 15 minutes, stirring once at the halfway point. Toss squash with remaining oil and season with salt. Add squash to the eggplant and continue roasting for an additional 20 minutes or until vegetables are fork tender. Remove from the oven and reserve.
In a food processor, add walnuts and pulse until finely ground but not paste-like. Add basil, mint, and garlic, then continue to pulse until finely chopped. With the machine running, slowly add the olive oil until a smooth paste forms, add additional olive oil if necessary. Add the lemon zest and season with salt and pepper to taste.
In a large bowl, combine roasted vegetables, freekeh and pesto. Serve and garnish with torn mint and basil leaves.