But that's taken from all the software available in the repos, not the software that's actually installed on people's systems. For instance, the pie chart shows slices for both Gnome and KDE. How many people have both installed on their systems? Or neither?
Now compare that to how many people have none of the GNU software on their systems.
I would imagine (purely anecdotal) if you take just installed software then the GNU percentage increases as its generally installed on most systems. I would also imagine in the Linux/BSD world the number of people running without GNU software is in the very low single digits.
It's really difficult to determine the relative importance of one software project at this level over another they reliant on each other. The Linux kernel needs GNU as much as GNU needs the kernel (at the moment anyway). You can run the OS without KDE (hence not calling it KDE/Linux).
I can see Stallman's point as he set out to create an operating system called GNU, created almost all of the parts required which were then used by someone else to create a Kernel which was then packaged up with a different name.
Personally I think you can call GNU/Linux whatever you want as the licence its released under has nothing in there saying you need to give mention to GNU in the name. If you package it up you can call it Fred for all I care and I will refer to it as Fred.
Actually in BSD/UNIX people generally don't use the GNU tools, except, maybe for gcc on BSDs (UNICES have their own compilers). We believe GNU tools are of very poor quality.
Now compare that to how many people have none of the GNU software on their systems.