> Well the first name used for the system was GNU, wasn't it?  

Then we should call it GNU - according to the Priority Principle. 
http://en.wikipedia.org/wiki/Principle_of_Priority 

There is precedence for changing a popular and well-known name.
Remember Brontosaurs?  Its name was officially changed when
paleontologists realized the name Apatosaurus was used first. 
http://en.wikipedia.org/wiki/Apatosaurus 
The fascinating story of bitter rivals and gigantic egos of "The Bone
Wars" 
http://www.suite101.com/article.cfm/4003/26156 
is detailed in the book "Bully for Brontosaurus" by Stephen Jay Gould.


Stallman is willing to accept GNU/Linux.  That's magnanimous,
acknowledges the work of others, and provides a useful distinction from,
say, a GNU/Hurd OS.