Well, either take my word for it or find someone you trust who's a pilot. They were not at any altitude that they didn't previously get permission to be at. But as they flew they'd get transferred from controller to controller as they enter airspace controlled by different controllers, and one of them commented on the rarity of seeing commercial traffic of that altitude. He'd already gotten a "strip" with all the flight's information, including their cleared altitude, on it. If the plane hadn't been at the altitude it had been previously assigned, the controller would have been much more concerned, as that would have been against regulations and potentially dangerous.
You were right, they got permission for FL410, its on the transcript Compilation of CVR, FDR and ATC radio transmissions and other events, on the NTSB investigation site. http://ntsb.gov/events/2005/Pinnacle/exhibits/CVR_Study.pdf
It was still irresponsible to slow the aircraft to 150knots though.
It's the pilot's responsibility to refuse altitudes that are dangerous -- but it sounds like these pilots requested the altitudes flown at.