GEM was just a GUI, which started on CP/M (and DOS.) The actual underlying operating system for the ST was Atari's own creation.
Of course I was simplifying..
I used to use GEM on the PC, so I was familiar with it from there.
But when people talk about the ST being stable, they are (IMHO) talking about TOS and GEM together.
When they are talking about the Amiga being less-than-stable, they are (again, IMHO) talking about the full desktop experience.
Especially since TOS does (as has been mentioned) virtually nothing without GEM.
That's like comparing TOS to the Amiga Kickstart.
Both of those were very stable. Both did nothing, but allowed other programs to do things.
TOS w/GEM seemed to be more stable than Amiga w/Workbench.
In that situation, GEM was a much more mature product, and didn't have to deal with the memory issues from a non-protected multitasking system.
However, that being said, I remember GURUs, but not that often...
desiv