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.
The transcipt on the site that you provided the link to doesn't contain any of the stuff in the yahoo article. Which one is correct?