Preheat oven to 450°F.
Rinse quinoa in a sieve under cold water for at least 2 minutes. Bring a pot of water to a boil. Add salt and cook quinoa for 12-15 minutes. Strain and rinse under cold water. Leave it in the strainer and set aside.
Cut peppers in half lengthwise and remove the seeds and core. Leave the tops on. In a large bowl toss with 1 tablespoon olive oil and sprinkle with salt and pepper.
Place pepper halves on a lined baking tray, cut side down. Bake for 8 to 10 minutes or until just starting to soften. Remove from oven, flip over and set aside. Reduce oven temperature to 350 degrees F.
In a large saute pan, heat 1 tablespoon olive oil over medium-high heat. Add red onion and cook for 2-3 minutes. Add garlic and zucchini. Cook, stirring for 2-3 minutes more.
Remove from heat and stir in cooked quinoa, tomatoes, olives, fresh herbs, and bocconcini cheese, 2 tablespoon olive oil, fresh lemon juice, salt, and pepper. Taste and adjust seasonings if necessary.
In an oiled baking dish, place the peppers together snugly but with enough room to add filling. Fill each pepper generously. At this point peppers can be covered and refrigerated overnight if making ahead.
Bake for 15 minutes or until filling is warmed through. Remove from oven and sprinkle with crumbled feta cheese. These can be served warm or at room temperature.