Statecraft is messy business. If you don't get your hands dirty you either don't matter or you don't last.
It is hard to judge these things fairly. Acting like we live in a perfect world and everyone who doesn't match that needs to be burned at the stake... well that's not helpful. Acting like the state gets a free pass for everything it does because being a government is hard makes us more and more terrible until something breaks.
Yes, a state in a leading world position needs to have a morally flexible arm to get things done, but that arm also needs to be regularly held in check, even if it's just for show.
The CIA and related agencies need pressure to keep them on their toes and doing the "right thing", but not expectation that everything they do will be entirely honorable. If you want that kind of thing, you have to move to somewhere small without much attention which has the luxury of honest opposition to all disreputable state behavior... because it is not in the position to be obligated to respond. (looking at you, smaller western Europe nations)