Toast the farro: Rinse 1/2 cup farro and allow to dry. Place the farro in a dry fry pan. Turn heat on stove to medium and toast the farro, stirring frequently until it is golden and fragrantly nutty, 10 -15 minutes
Bring 2 cups of water (or broth) to a boil. Stir in the toasted farro and return to a boil. Reduce heat and simmer until most of the liquid is absorbed, 30 minutes or so. The farro should be chewy but tender. Drain any remaining liquid and set aside.
Heat a soup pot over medium high heat. Add the olive oil. Once the oil is hot, add the onion, garlic and red pepper flakes. Stir to coat with the oil and cook for 5 minutes or so until the onion begins to soften.
Stir in the stock, tomatoes, Italian Seasoning, and Marsala. Bring up to a boil and reduce the heat to simmer. Simmer for 20 - 30 minutes. Use a potato masher to create a chunky soup. Hit it with the immersion blender if you want it smooth.
Stir in the farro and beans. Simmer for a little longer; 15 minutes is about right.
Ladle into soup bowls and garnish with the pesto and croutons if desired.