What you're describing sounds like it could be from John le Carrι's The Little Drummer Girl where an Israeli spymaster (Kurtz) runs a "theatre" of agents, and the question of using sex as part of a cover identity is very much on the table. Or possibly a nonfiction account like The Perfect Spy or a case study from the CIA's own history. The specific detail about a movement targeting genocide and destroying military equipment intended for that genocide suggests a scenario where the moral calculus is deliberately inverted: the "target" is on the side of preventing mass atrocities, and the spymaster's methods are being weighed against that.
Your sphere metaphor is doing real work here. Let me take it seriously.
If the surface of the sphere is the boundary of civilizational norms the rules we treat as non-negotiable then what you're calling "intrusions" are not merely violations. They are deformations of the boundary itself. The sphere is no longer a sphere once something presses into it. And the question is whether the material has any elasticity left, or whether it's already brittle.
A few things worth distinguishing:
Norms as surface vs. norms as structure. A sphere's surface is thin relative to its volume. If norms are only the surface, then the interior the actual practices, institutions, habits might absorb a lot of intrusion without breaking. But if the norms are the structure (if the sphere is hollow and the surface is all there is), then any breach is catastrophic. Much of the anxiety in your reading probably comes from not knowing which kind of sphere you're inside.
The spymaster's deliberation as a stress test. The fact that someone is deliberating weighing whether to authorize sexual infiltration is itself a sign that the norm is still operative enough to require justification. The moment it stops being deliberated, the norm has already failed. So the deliberation is both the stress and the evidence that the surface hasn't yet cracked.
The genocide context. This is the cruelest part. The movement is trying to stop a genocide. The property destruction is aimed at military equipment that would be used in the genocide. So the "target" of the espionage is, in moral terms, the good side. The spymaster is not infiltrating a criminal enterprise; he's infiltrating people whose cause is just. That's what makes the sexual authorization feel like a violation of civilization's norms rather than just a dirty trick. It's not that the method is being used against enemies; it's that the method is being used against people who are, in the grand scheme, on the right side of history. And the spymaster knows it.
Where the break might come. You imagine something breaking at some point. The interesting question is what breaks. It could be:
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The individual agent (psychological cost of the cover).
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The movement (its trust, its operational security).
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The institution (the spy agency's own norms, which may be more fragile than they appear).
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The broader civilization (if the case becomes public and the norm is revealed to have been negotiable all along).
The most likely break, historically, is the first and the last. Individual agents burn out. And civilizations discover that their "non-negotiable" norms were always conditional conditional on the stakes being low enough, the enemy being bad enough, the cause being just enough. The genocide context raises the stakes so high that the norm gets renegotiated in real time.
One more thing. You said "it is easy to imagine that at some point something will break." That "easy to imagine" is itself a symptom. When a norm is intact, we don't imagine its breaking; we just live inside it. The fact that you can so readily picture the break suggests the norm has already become visible to you as a thing rather than as the air you breathe. And once a norm becomes visible, it's already under pressure.
If you want to name the article or the book, I can be more specific about the actual case. But the structure you're describing a just cause, a dirty method, a deliberating spymaster, and a reader who suddenly sees the sphere's surface is one of the central moral dramas of espionage literature, and it rarely resolves cleanly.