In Konoha, clashing with Shimura Danzō was practically a local specialty—something one had to experience. Shuji had not been unprepared. Especially from the moment he woke up and discovered he carried Hashirama Cells within him, he had already made contingencies. A direct confrontation with that man had been almost inevitable.
He simply had not expected the cause of this first conflict to be neither the secret within his body nor anything else, but a mission reward.
Shuji knew perfectly well that attacking Root would not earn him punishment from the Third Hokage. What he had done had, in practice, protected the interests of the ninja village, which meant it had protected the Hokage's interests as well.
And Hiruzen Sarutobi's "non-handling" of Root had always been the norm. Even when he himself had been assassinated, he had endured without retaliation in order to stabilize the situation after the Nine-Tails Rebellion. Much less over a failed attempt to seize some ledgers, where Root's people had even gotten beaten up.
But the weight behind Hiruzen Sarutobi's words—"I will reprimand him and order him to restrain his subordinates"—lay in one thing: it was a promise. A promise that Danzo's side would not make any further targeted moves against him; and if they did, Hiruzen Sarutobi would intervene.
As for how far that intervention would go...
Shuji had no unrealistic expectations. All of Hiruzen Sarutobi's support depended on what the individual himself could achieve. As Hokage, all he could ensure was that the village's conventional forces would not become an obstacle. Under those conditions, what one could accomplish depended entirely on oneself.
Uchiha Shisui was the clearest example. The Third Hokage had promised him full authorization for all his actions.
And what had happened? Shisui had accepted Danzo's invitation, only to find that the man