1. Combine 2 quarts water and salt in a large saucepan or Dutch oven; bring to a boil. Cut bottom halves of green onions into 4-inch pieces; reserve tops for another use. Add green onions to water; cook 30 seconds. Plunge into ice water; drain. Divide green onions equally among 2 (1-pint) mason jars. Divide rind and thyme evenly among jars.
2. Combine vinegar and remaining ingredients in a saucepan; bring to a boil. Reduce heat; simmer 5 minutes, stirring to dissolve sugar. Divide vinegar mixture evenly between jars; cool. Cover and chill at least 24 hours.