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There’s two threads running in parallel here, the retrocop thread and the naomi thread.
The naomi thread’s line seems to be that we kill spies because a) we can, b) the ‘law’ is on our side, c) they might manage to smuggle secrets out of their prison cells, d) they are really bad people and don’t deserve our humanity, and e) (unspoken but I’m sure implied) that they are FOREIGN.
The retro/mushroom/jim line is less dogmatic, as you’d expect from the thinking side of these columns.
I’m not sure there is an ‘answer’. Except, I suspect, vindictiveness - my view being that most spies were just foot-soldiers, as guilty or innocent as any other. And often, even braver!