We have two different elements here. Banished! Naruto and MobsInKonoha!
For Banished Naruto, the only way it works is if he is in on it, and Konoha is using it as an excuse to let him go around freely or spy for them. Even under those circumstances, it is still hard to believe, but tolerable because Konoha has been top dog in the EC for a long time, and never felt the need to field Kurama or his host as a weapon. So if they were suddenly lacking Naruto, I don't think it would matter much, except that the other villages may want to hold their own jinchukiri a little closer to their chest so they don't get nabbed (keep in mind that if they kept Sasuke in any way, or could call up Itachi, or just use Yamato they can get the biju under lock and key without having to try very hard, making killing the host a tenable option.) If the other villages have any intel on Konoha.
To be honest, I don't really like the Dark and Grey theme for Naruto, because Konoha as a unit is competely bad ass. Assuming they don't have to worry about public relations (logical extension of a military dictatorship) Itachi takes down the rest of the clan, then sticks around to help raise Sasuke. He can just say the answer is classified, or tell Sasuke the truth. Itachi is a monster of the highest level in the manga, but ignoring him (stupidly) let's see who else is in the Konoha roster...
Jiraiya who is such a harass two S rank ninja didn't think that they could double team him and win.
Tsunade who wouldn't be allowed to leave, and is no joke.
Kakashi, who has the potential to be better than his father, who was the equal to ALL three Sannin. Who has also copied 1000 or more techniques, and is a certified bad ass without his hax eye.
Yamato who has the ridiculously OP vs jinchukiri and biju, and was an ANBU captain beside.
And that's just the players that we know are 5/5 stars of rape vs. Most ninja. I find it hard to believe any village that has that much destructive capability is afraid OD anything. In fact, I would fully expect them to set up a kill squad and harvest the biju the first Hokage gave away and reseal them into 9 individuals from Konoha.
The only reason that this setting works is because it is a good and evil setting, otherwise the imbalance of power in Konoha (think about it, how many badasses come out of Konoha compared to all the other villages put together? Most of the big players of Akatsuki are either Konoha trained -Nagato, Konan, Orochimaru, Itachi- affiliated because of Konoha -Tobi, Deidara, Kisame- or haven't been able to defeat a Konoha based team -Hidan, Kakuzu, Sasori, Diedara again- of people with lesser ranks) would let them just take over the world.
Which basically rules out mob scenes unless there are extenuating circumstances. Here are a few, Naruto has a different life because of the seal (he ages faster towards his prime, has enhanced senses and physical make up, doesn't eat or drink like a normal human) that sets him radically apart, and then somethig bad happens that would turn public opinion against him. For instance, he hurts or kills someone with super strength, is a public hazard in some way, or some other traumatic event that spurs some kind of reaction against him. I like the fact that my country has bikes pointed at my enemies, but if I think that nuke is pointed at me, I might not like it so much. Take it even further though, and have an enemy agent come in and using infiltration tactics and genjutsu, is actively starting mobs and creating a counter-culture that is against using children as weapons.
Then we have a dynamic where there is danger to Naruto as an individual (mobs under coercion are trying to hurt him) which are easily dealt with, but also as a military asset (they are being nice to him, and advise him to become something other than a ninja) which can't be. The mobs should be the symptom of a larger conspiracy, not a cause and effect chain of themselves.
Jeez this got long. I wonder if I should add a bit of butter and serve this up over in the ideas thread for someone to use.