Honestly, from reading that, it's not clear why this would be a story worth covering. Corruption in Iraq is like rain in Seattle: Depressing, but barely newsworthy.
Since D-notices are not legally binding, if The Guardian received one but chose to report anyway, I'd be very surprised if they didn't mention a D-notice - the times government have overstretched with respect to D-notices, it has usually caused a major stink.
The Guardian is wholly owned by a UK trust, and its head office remains in London.
The only thing that changed was that reporting of the Snowden affair was shifted to their US office. The Guardian pointed out to GCHQ in advance that it made no difference as they already had copies of the data elsewhere.
Furthermore, it was The Guardian itself who "ground up" their computers, as they refuse flat out a request to let GCHQ inspect the computers and do the destruction. Instead they agreed to destroy them in the presence of GCHQ staff, exactly because it didn't matter, and let them avoid legal liabilities. And frankly being able to put the story in the paper probably didn't hurt. From the article you linked:
'"Three Guardian staff members – Johnson, executive director Sheila Fitzsimons and computer expert David Blishen – carried out the demolition of the Guardian's hard drives. It was hot, sweaty work. On the instructions of GCHQ, the trio bought angle-grinders, dremels – a drill with a revolving bit – and masks. The spy agency provided one piece of hi-tech equipment, a "degausser", which destroys magnetic fields, and erases data. It took three hours to smash up the computers. The journalists then fed the pieces into the degausser.
Two GCHQ technical experts – "Ian" and "Chris" – recorded the process on their iPhones. Afterwards they headed back to GCHQ's doughnut-shaped HQ in Cheltenham carrying presents for family members, bought on their rare visit to the capital.
"It was purely a symbolic act," Johnson said. "We knew that. GCHQ knew that. And the government knew that," He added: "It was the most surreal event I have witnessed in British journalism."'
