Place greens, chopped onion, red pepper, and smoked ham in a large stockpot; cover with water to 1 inch above greens. Bring to a boil over medium-high heat. Uncover, reduce heat, and simmer for 1 1/2 hours. Drain greens in a colander over a bowl, reserving 2 cups cooking liquid.
Combine low-fat milk and all-purpose flour in pan, stirring with a whisk until blended. Stir in reserved cooking liquid, salt, and ground black pepper; bring to a boil over medium-high heat. Reduce heat, and simmer 3 minutes or until mixture thickens, stirring constantly. Add greens; simmer 10 minutes, stirring occasionally.