The article doesn't say that NASA destroyed the rocket; only that it was destroyed, and the cause was unknown. Most likely, it just exploded, as
rockets sometimes do.
Pity, though, I'd have liked to see the results of their hypersonic tests.
The launch marked the first and only flight of the ALV-X1, a rocket ATK built and paid for to test various proprietary technologies Rominger declined to identify. NASA's Hypersonic Boundary Layer Transition (HYBOLT) and the Sub-Orbital Aerodynamic Re-entry Experiment (SOAREX) payloads were on board the nearly 55-foot (17-meter) tall rocket.
The HYBOLT experiment, developed by NASA’s Langley Research Center in Virginia, was aimed at studying the effects of airflow and heating on hypersonic vehicles designed to fly at velocities faster than eight times the speed of sound.
NASA’s Ames Research Center in California designed the SOAREX experiment, which consisted of three separate probes that were expected to be released after HYBOLT was jettisoned, then plummet back toward Earth to evaluate new techniques for spacecraft reentry.
One of the three probes belonged to the U.S. Naval Research Laboratory and carried prototype receiver and transmitter for use in tracking objects in ocean recovery, NASA officials said. There are currently no launch-worthy spares for the experiments, they added.