Well, firstly, the GBU-28 can penetrate to 100 feet of earth or more (granted, it's heaver by a few thousand pounds), so there's no reason a nuke couldn't be built to the same specs. Secondly, the author was talking about a miss with a 10 kiloton device, but the the B61 family of weapons can be configured with a wide variety of yields, including 0.3, 1.5, 5, 10, 45, 60, 60, 80, 170, and 340 kilotons. What you lack in accuracy could be made up for in tonnage.