Say rather, the thinking goes “if one does it, and he is denounced and appropriately disciplined (fired & criminal charges), then the problem is with the officer, not the department. If one does it, and he is not named by his department nor does his department fire and imprison him for his crimes, then the department is to blame.”
When the department does not do so, the implication is that the entire department is littered with those who have repeatedly violated the Constitution, and they wish their crimes to remain hidden.
That's why it MUST be stopped and publicly denounced. Otherwise, it's corruption is as corruption does and all trust and goodwill is lost, for all the reasons you cite.