Set programmable pressure cooker to SAUTÉ. Add rinsed and drained beans, and 6 cups water. Bring to a boil and fasten and lock lid. Switch cooker to HIGH PRESSURE for 1 minute. Release pressure manually and carefully drain beans. Transfer beans to a bowl, and set aside.
Place cooker insert back into programmable pressure cooker base and set to SAUTÉ. Add oil and sausage; cook 7-8 minutes, stirring occasionally, until sausage begins to brown. Add onions, garlic, and thyme; cook 4-5 minutes, stirring occasionally, until onions are translucent. Add beans, stock, and salt. Cover programmable pressure cooker and fasten lid. Lock and seal steam valve. Set to HIGH PRESSURE and cook until beans are tender, 10 minutes. Release pressure manually.
Uncover programmable pressure cooker, stir in kale, pasta, zest, crushed red pepper, and tomatoes. Fasten and lock lid, set cooker to HIGH PRESSURE and cook for 5 minutes. Release pressure manually. Serve in bowls topped with cheese.