Heat the oil in a large pot over medium heat. Add the red onion and ¼ teaspoon salt and sauté for 4 to 5 minutes until softened.
Add the garlic, 1 cup tomatoes and black pepper and sauté for 2 to 3 minutes, until the tomatoes start to burst.
Add the fregola and toast for 3 to 4 minutes, stirring frequently to prevent sticking.
Add the vegetable broth and remaining salt and bring the mixture to a boil. Simmer for about 10 to 12 minutes, stirring frequently to prevent sticking, until the fregola is al dente. If the liquid is absorbed before the fregola is tender, add additional broth (about ¼ - ½ cup) and continue cooking until done to your liking.
Turn off the heat and add the balsamic vinegar, remaining tomatoes, green onions, and basil. Stir to heat through. Taste and adjust seasoning, if needed.
Stir in the nutritional yeast or vegan parmesan, if using. Serve immediately.