Yes, they are. Same reason as him too.You have the Hokage, The Konoha Council (the two old farts) and Danzo who controls much of the secret poilice apparatus if you will. The Konoha Council were emboldened enough to go against Sarutobi's wishes and side with Danzo. They apparently didn't fear facing any repercussions from the Hokage for doing so. Are those two old farts also impossible to punish or kill like Danzo?
When you're the strongest ninja in the ninja village, and you have an alliance with the strongest ninja clan in the village, no, you don't worry about the guy in charge of the secret police. You politely remind him that there's a reason you left him to do the black-ops work, and it wasn't because he knew how to operate in overt warfare. You then point out to him that if he attempts to subvert that alliance in anyway, he can look forward to the other clans of Konoha taking umbridge to such an explicit condemnation of their lifestyle.Sorry, I am not sure they would feel any less inclined to go against him even if the Hokage said things were resolved. That is the problem with miliatary or police states, the guys in control of the secret police (Danzo) tend to be the guys with the real power. Given all the real world examples of miliatry/police states, I think it is naive to think reason wins the day once the guys in charge of the secret police decide you are a threat.