It's always important to force yourself to remember that essentially all detestable acts are done for detestable purposes, no matter how selfless the rhetoric tries to make them sound. There may have been a handful of exceptions in history, but they are so vastly outnumbered by the other kind that they can safely be ignored.
The narrative of doing something for the greater good should be treated as a lie until the burden of evidence is so high that you are forced to accept that it was indeed good. In particular, spy agencies have produced far more terrorism, coups, and disinformation for their own people, with the goal of supporting the monetary interests of their nation, all others be damned, than they have ever defended anything. The exceptions almost always happen when the goals of empire happen to be aligned with those of the people, like during WW2.
An obvious impossible standard, more than that you can’t really know if an action was right or wrong without an oracle to tell you what would have happened if different forces had been made.
Nations can’t just disappear, anarchy always transitions to tribalism to monarchy to ... etc.
Rewriting my entire home operating system to be the ideal may be a fool's quest, because one person will never be able to do as much work as the hundreds or thousands who developed the code he is replacing, but if you want to try it is entirely on you. I can putter away in my basement for years without bothering anyone.
Replacing or reforming a political system is fundamentally different because it requires the buy-in of a large portion - a super-majority ideally, but at least a powerful minority if you're willing to play violent or dirty - of the population to get started. And you can't just show up out of the blue with A Plan and expect people to all be on board - even if your plan is really quite good, human nature means almost no one will want to commit to someone else's plan. So you have to develop your plan in a group, making compromises that you may personally disagree with to get larger and larger groups of people on board, until, unless there really was a large number of dissatisfied people in your camp all along - which we all want to believe but is seldom the case - you end up politicking your way to a revolution that is barely different than the status quo.
Because we ourselves, our bodies, are an emergent system rather than a designed one?
Human biology seems to be even more chaotic than various political systems on Earth, but both have one great advantage under their belt: they survived unexpected crises in the past.
Designed machines tend to be nowhere near as robust.
Such organizations are simply necessary to run a nation. Global politics is a game, and everyone plays it. It involves gathering intelligence and acting on it. The work isn’t beyond reproach, and the nature of secrecy makes doing dirty things an unavoidable consequence... but ultimately you have to accept that reality is messy, the world isn’t very nice, and sometimes you don’t have a choice as a nation but to do some detestable act for some higher purpose... and rarely will it be possible for the whole story to be told publicly in order to be judged fairly.
Sure it would be nice if everybody stopped being so awful to each other, but you can’t pretend like that is already true if you don’t want to lose everything.
In plenty of circumstances intelligence agencies have done things that never should have been done, but that isn’t an argument to stop all together.