Well, I think the fallacy is to look at any nation, let alone of any of its government's constituent parts, as a monolithic entity in terms of ideology and ethics. Even Israel is not a special case, nor their various agencies and departments.

Rogue factions with access to the right intelligence and or means can accomplish their own goals despite not having a quorum of inside support. They can also navigate plans with the optics in mind that if those sorts of schemes were disclosed it would reflect badly on the whole rather than a single faction. This is key for the more radical factions trying to sow enough chaos and conflict as a means to some other end. Throwing their whole gov't or even nation under the bus, at least in the eyes of some of the world, would not be out of the question.

In the meantime there are metaphorical white hats / patriots in every government and military complex, but history plays out in a way that they don't often have the upper hand, or access to the levers of power for good. Maybe they do more often than we think and that's why we don't hear more bad news than we actually do?