In a medium saucepan, bring cranberries, sugar, molasses, and thyme to a boil over medium-high heat, stirring frequently. Boil, stirring often, until most cranberries pop, 5 minutes. Remove from heat and stir in pomegranate seeds. Discard thyme.
*Buy at well-stocked supermarkets and Middle Eastern grocery stores.
Make ahead: Chill cooked cranberries, covered, up to 1 week; add pomegranate seeds just before serving.
Note: Nutritional analysis is per 3-tbsp. serving.