I do know about the whole "ignorance is bliss" stuff, but everytime something comes at the surface, the responsible ones are the ones who run the country... and I wasn´t quite aware of how all those organizations function, I just meant that they´re loyal.
Now, I don´t remember all of Root´s history, but seeing how Danzou ultimately wanted to take over power himself and had his own group of brain-washed ninjas, I wouldn´t quite compare them to other real-life organizations. I also don´t know if what you said about ANBU is entirely accurate, since they are the ones who take care of "accute problems" (Root was founded by Danzou, wasn´t it? Before that, there wasn´t such an organization...so who would have taken care of those problems otherwise?). I might have to read a wikia article or two tomorrow.
What secret services and other intelligence agencies do is quite...disturbing. I´d say it is necessary, but we don´t really know if it always is. And innocent people are mostly the vicitims of doubtful missions.