It chastises the behavior of those people while praising their own behavior, even though it's essentially the same.
It sees heroes in spies, even though they are villains.
Each side thinks, that they are on the right side.
Edit: Even though the novel tries to point this out a little, it still uses all of the above to great effect.
All governance systems are imperfect, but some are more imperfect than others.
Although he is fascinated by the craft of spying (and I can see why some people might find that objectionable or regrettable) Le Carre does not engage in the moral stereotyping or moral certainty you describe.
Also, spies probably save lives: if for example the Kremlin had been more skilled at collecting and analyzing information about Ukraine's military capabilities, they probably wouldn't have invaded.
I am one of those people. We didn't get to choose, but most of us hated the regimes that ruled us. I am fine with their portrayal as prisons of nations, because that is what they were. No need to whitewash Communism.
The Soviet empire was brutal and evil, and I am not at all surprised that a former KGB thug now started the biggest land war in Europe since 1945. It perfectly fits the imperial mentality of the Siloviki [0], who all made their early careers in Soviet armed forces and secret police.