Place lima beans, thyme sprigs, onion half, and garlic in a medium saucepan, and cover with water. Bring mixture to a boil over medium-high heat; reduce heat to medium, and simmer, stirring occasionally, 20 minutes or until beans are tender. Drain beans, reserving 1/2 cup cooking liquid. Discard thyme sprigs, onion, and garlic.
Sauté diced onion in hot oil in a large skillet over medium-high heat 5 minutes. Stir in corn and honey; cook, stirring often, 6 minutes or until corn is tender. Stir in beans and 1/2 cup reserved cooking liquid; cook, stirring occasionally, 5 minutes. Stir in butter, and add salt and pepper to taste. Sprinkle with chives.